Captain SNES/WMG

When the story reaches the Final Fantasy VI world, it will turn out that Cyan is Touched
While just about everyone in that game is in serious need of a hug, Cyan is the perfect candidate for a position as a servant of the Shard of Tears. Sorrow and loss defines his character; in the span of a single day, he lost everything he had cared about, and he continued to blame himself for a long time: for what happened to his family, what happened to his kingdom, and what happened to the world. This is pretty much the definition of the Shard's power; always looking backward, never forward, dwelling on the past. Also, Wexsoul will be another servant of the Shard; as a monster formed of nothing but raw sorrow and hatred, he is another perfect candidate.

Terra will be pulled from the Final Fantasy VI world into a world with still-working magic
Once she does, her Esperkin magic will come rushing back to her, and the sudden overload of magic will result in her going "ballistic" again.
 * Close., and now magic exists again. Something happened to Terra, not clear what.
 * I think she reverted to her Esper self.

The "Eater of Dreams" and the "Dream Devouerer" will have something to do with each-other
So what if Chrono Trigger DS didn't exist when the Eater of Dreams was first named?

The "Sovereign of Sorrow" is not dead
Not only is it alive, Ryan K. has been touched and the Sovereign is playing two of it's biggest threats against each other as it has been doing throughout the storyline.

Ryan is Touched by the Sovereign's counterpart
Two main reasons for this- Ryan speaks in green, and can hear Captain N!Mega Man. Hope-Touched Roll spoke green (OK, it was half green/half purple, but still) and alpha energy's visibly green. It also fits with his worldview, and would work with the theme- alpha energy has been described as "corrupting" too, and he seems somewhat naive-; what better way for someone to be corrupted by excessive Hope than for them to see everything in black-and-white fantasy-style good and evil, where the heroes always act like heroes and always win?

Ryan has been touched by both the Sovereign and her counterpart
Unlike Roll, he doesn't have both sides, it manifests by him having the innocent worldview and black and white morality, but signs of corruption of the Sovereign are his complete inability to recognize things. Alex sees some of this, but can't put two and two together.

The Sovereign is Hope Keene
There have been numerous references to Hope Keene, and she's yet to actually appear in the story. It seems likely that the climax of the story will be Alex learning that Hope is in fact his enemy and being forced to battle against someone he cares for.

Hope Keene is the Sovereign's opposite number
Based solely on the name, but it seems a rather large coincidence that we have the opposed forces of Hope and Sorrow and a significant character called Hope. Could still do as above, as the hope side is described as corrupting too.

Bowser's been touched by the Sovereign's counterpart
Because just about the only way he could possibly believe he stands a chance of winning at this point is by being empowered with the very essence of hope. Also, it would explain why his son seemed relatively cheerful compared to the rest of the touched-being related to bowser granted him some degree of protection.

The Sovereign is a
In the latest comic,

The Sovereign is the ghost of Gunpei Yokoi
The Sovereign can see the future, but not the past -- which, in The Divine Comedy, is listed as one of the abilities of the damned. The sovereign also has access to Game Master-like powers, can change the abilities of sprites (even if limited to only improving pre-existing abilities), and gives knowledge of the real world to anyone Touched. Clearly, the Sovereign is Gunpei Yokoi trying to take revenge on the company that destroyed him -- the whole female thing is a misunderstanding caused by using Queen Zeal as A Form You Are Comfortable With for Magus.
 * And using Princess Peach for Roy Koopa.

Related to above: The Sovereign has something to do with/is
This makes perfect sense if you look at how the universe appears to work: no console is capable of modifying the game programmed into its cartridges on the fly, it takes. Thus, the Soveriegn is able to override the built in rules of the carts, allowing, among other things, Lucca to deal damage in hex. The Sovereign could have been created, intentionally on not on the part of the requisite Game Master, out of the divide between

As an alternate to the above: The Sovereign has something to do with/is
She can edit reality. She can also destroy reality. Also Touched characters can see beyond the fourth wall.

The cat is a Game Master.
It already has been shown to have ridiculous skill, it has stopped the prediction of the future, because people can't see it, and it was said to arrive the same way the other Game maters arrived. It was not a fluke. The cat was meant to save them all. Only later. At a more climactic time.
 * As Bonus evidence, I present this page: . Please, doesn't that bio for the cat look too suspicious for the cat NOT to be a very important character (at Game Master level).
 * Alternatively, the Cat is the Game Master's familiar, like what Duke was.

Mega-Girl dies next.
There were three lost that day, including Mother Brain and most likely Duke. Wily, Eggplant Wizard, and King Hippo are accounted for, while Mega-Girl dies at an unspecified time. I guess she is a decent potential victim in this battle.
 * Wily basically does a Look Behind You! that Green doesn't believe, but one of the other villains shoves her into the Omega Warp while Green's not looking.

Omega Energy is anti-Narrativium
Basically, it's the ability to override the laws of narrative causality. Originally, Captain N was an immature 80s kid's show, so no one died permanently (they occasionally lost an extra life). Then Mother Brain harnesses Omega Energy, and now the bodycount is going to start piling up. And because Captain N hailed from the Real World, he brought it with him, hailing from a universe where there is no overarching story.
 * It would naturally follow that Alpha energy is Narrativium.
 * Maybe the formation of video game characters is due to a material similar to Deitium?

Alex will steal Setzer's deck.
Because there's no way that mention of a pack of cards making him invincible was just a joke.

Cecil will escape with the help of Kappa the Imp.
Cecil will ask him to demonstrate how to flee, which Kappa will happily oblige.

Ryan understands Crono.
He's demonstrated an understanding of Green. Why not other SPS sufferers?
 * This is explicitly shown to be true

Ryan will start translating Crono.
Extrapolating from above.

Ryan understands Heroic Mimes because he thinks of them differently than Alex does.
Videoland is meant to be affected by the interpretations of the Gamemaster. Alex seems to think of silent heroes as actually silent, except that the people around them understand them. Ryan is probably one of the people who thinks there is implied talking and maybe even puts words into their mouths while playing games. Ergo, he thinks he should understand them and so he does while Alex thinks he shouldn't and doesn't.

Samus won't let Eggplant Wizard die not because she's going to horribly brutalize him.
Samus won't let Eggplant Wizard die because it will mulch an innocent in his place. The horrible brutalization that she will inflict upon him is merely incidental.

Alex's bit about Chozo Mental training is a Chekhov's Gun.
Alex will use that to his advantage.
 * "Ignore the cat".

The pants that Protoman gave to Alex in episode 694 have a deck of cards in their pocket.
Which means that Wily's nigthmare just came true.
 * It's mentioned in the present that Alex does have a deck of cards with him...

King Hippo was touched by the Sovereign of Sorrow.
Seems to be implied by Spoony in episode 390. Spoony says that prolonged contact with the power of Sovereign of Sorrow "tends to make one a bit loopy" and that he has "no particular desire to [run] around blasting druggies or drinking insane amounts of beer". Part of this sentence is obviously an allusion to Max Force, who is confirmed to be touched by Sovereign, while the part about drinking beer fits King Hippo. Thus, he seems to imply that King Hippo had a contact with the power of Sovereign, and most likely was touched just like Spoony and Max Force.
 * I think it's Seraphina, given that she was working with purple-eyed Zelda and one of the reasons she and Hippo divorced was because she kept stealing his beer.

Light built X under the influence of being Touched.
That's why his series so much more angsty than its predecessor.

Bob is Prince Lyle.
Prince Lyle is believed to be MIA and the last anyone saw of him, he was in what became the Desert of Broken Dreams. Given his huge expertise on what is going on and is implied to be one of the Voices (lost souls who have forgotten their names) and his description as a being with two souls, Bob is Alex's character from the Game Boy FF game possessed by the voice of Prince Lyle.

Simone did not, in fact, kick Captain N into a warp to the Mirror World.
This comic is one big flashback with flashbacks inside, with plenty of bleak scenes, yet it's almost never colored in Monochrome Past. But both times (so far) Simone's betrayal is depicted, it's Deliberately Monochrome. In comic #311, Simone seems surprised that Kevin is around and starts to deny... something. And as of comic #703, I'm starting to get the impression that the story is a little fishy.

Both Ryan and Hope from the real world are somehow relatives of Kevin Keene, the original Captain N
Not only have do all three have the same last name, but we know that Kevin actually DID have a child named Hope. It would explain why Ryan can understand silent protagonists, since Captain N could, too.

The Shadow King is Bob.
We already know Bob has a mysterious past, tied up somehow with the Sovereign of Sorrow. In his own words, here: http://www.captainsnes.com/2002/04/02/094-capn-tells-it-as-he-sees-it-2/ he seems to have a past that is not only dark, but seemingly actively villainous in nature. On top of that, as seen here: http://www.captainsnes.com/2003/05/13/332-the-omissions-are-the-interesting-part/, Bob obviously has great knowledge about the Sovereign of Sorrow, and he still seems to be able to harness Omega Energy, power which is the signature of the Sovereign. Also, he mentions Videoland suffering because of his weakness, which would suggest that Bob is now The Atoner for some past horrible deed. So, here's what happened in the past. Bob, in his own world and on a quest for some sort of ancient, forbidden magic, discovers the dormant Sovereign of Sorrow, and decides to release and serve her in exchange for power. One of these powers is, obviously, immunity to the Sovereign of Sorrow's energy, and possibly shapeshifting, powers which he seems to have retained (this may be a sign that Bob may still be on the Sovereign's side; we already know that Alex is meant to play a part in the Sovereign's rise, so Bob may just be one of her servants sent to help things along, and in doing so, help Alex in any way he can). So, a clever shapeshifter like Bob could certainly be useful for the Sovereign's plans; so, they hatch a plan to sow chaos among the residents of Videoland. So, they tell Mother Brain about Omega Energy, and the nature of the world: Mother Brain's already evil, so she isn't affected by the Sovereign like other characters are. A picture of someone is the key to unlocking this energy, and it has somehow fallen into the hands of Space Pirates, so they get Eggplant Wizard and King Hippo to fetch it for them. Now, Bob and the Sovereign both still need to stay hidden, so they make it look like Mother Brain is the one coming up with the plan in the first place; the true purpose of letting Mother Brain know all of this, rather than trying to help her conquer Videoland, was simply to extract the Omega Energy for the Sovereign; the winner of the conflict between Captain N and Mother Brain was irrelevant. The gathering of the villains may or may not have been a part of Bob's plan, but after Mother Brain's death, the villains are now under the control of Bob and the Sovereign of Sorrow. Bob, now going as the Shadow King, would naturally be difficult to catch, since he has shapeshifting powers, and would simply take an innocuous form between evil schemes. Also, since he controls the Omega Energy (remember, we never found out what happened to the Omega Energy after the destruction of the Metroid), he effectively has control over every world in Videoland, and all the N-Forcers can do is follow his inept goons on small missions while the Shadow King does his real villainy elsewhere, unimpeded.

So, what caused him to turn from the Sovereign's side? Ultimately, we'll just have to wait and see...
 * Well, The Shadow King never was on her side. It was a case of Evil vs. Evil.

Protoman is Sorrow-touched
Alex referred to his world as the "real world" a couple times, and Protoman didn't react. The only explanation for this other than a writing slip-up is that he's sorrow-touched, which tends to cause sprites to realize their status as video game characters, and are "not real".
 * He's a veteran of decades of work with Keene and against the Sovereign. He might dismiss that as a quirk of Gamemasters and the Touched. Or he's badass enough not to care.

Lana is the Sovereign of Sorrow
First, start at #707, seventh panel; someone described the Sovereign as looking like Lana. At #576, the silhouette is no longer Schala, but Lana. Furthermore, Princess Hope describes the rapid destruction of game worlds as "the price of my failure"--and it was previously noted that she tried to convince Lana not to go after Kevin. Kevin's explanation of what happened to Lana is suspiciously unspecific: "The Sovereign took her from us." While some might think this is a way to avoid saying "She's dead", a clue is that he fumbled around for a few panels. Think Darth Vader. In a manner of speaking... As to why, if Lana is the Sovereign, she is immune to Omega energy unlike her subjects, I point this out: There is no such game character as Princess Lana. The royal family was created in the same way as Captain N--by the creation of a cartoon. Remember that Alex used to watch said cartoon! Finally, the Sovereign's description of Alex is peculiar: "He is the champion of Videoland. He is my champion." And of herself: "I am Sovereign over a world of sorrow." Who says the Sovereign is not speaking literally? This just leaves the question of who was the King of Shadow, that finding out his identity would send her spiraling into omnicidal madness.
 * He never SAID she was dead. Everyone else jumped to conclusions when he wouldn't answer them.
 * Clearly, it was her dad.
 * Which leads us to the next:
 * Also note that on the Sovereign's official Bio, her job is listed as Princess...

The King of Shadow is King Charles
The story of what happened in the Mirror World after Mother Brain's demise is fabricated by Kevin. Something went horribly wrong when Kevin tried to pull Charles out, but somehow it did...something nasty to Charles. Having a reputation as a perfect hero, Kevin can't bring himself to sully that by admitting to a hideous mistake, so he made the whole "died to send me home" story up. Simone, for all that he was a donkey, wasn't lying when he said Kevin just disappeared, either. What makes this persuasive is that "dead for real" is only possible in Videoland through use of Omega energy--which, at the time, only Kevin could access.

Mario is not what's stopping the Sovereign
Or at least, not the only thing. Sure he's powerful, but he's merely the Optimus Prime of Videoland, and he is facing what is essentially the Unicron of Videoland. Against such power, only the Autobot Matrix of Leadership of Videoland can stop her. Which is clearly... The Cat! Basically, something from the Primus(es) of Videoland to help light their darkest hour.
 * Proof! Mario knows The Cat!
 * The Sovereign's not the only one who has The Touch.

Simone Belmont was the Shadow King
I just think it fits. He was banished right before the Shadow King showed up, after all.

Captain N himself is the Shadow King.
The sprites are somewhat similar, and other than Captain N, who else had access to that power? Also, his strange attitude leaves a lot to consider. Alex had a very good point. N seemed downright unconcerned with losing Lana. To the point that it took his daughter demanding his attention and questioning him on where she was. And Kwirk the Tomato even stated that Captain N was the one who called the Sovereign there in the first place. Granted, he was touched, and trying to scam people, but that doesn't mean he may not have been right about that bit. How else did he know about it?
 * It's a good idea, but not quite right. There was a cell that showed both Kevin and the Shadow King in the same location. However, it could have been his Mirror-World alter-ego.

Magus will give the Shard of Sorrow to the Sovereign.
It's pretty obvious that the sprite used for the Mask of Tears is Schala. But if Schala is truly the host for the mask, it could explain why the representation that spoke with Magus stated it could not see her future. In all likelihood, if Magus does meet up with her and recognizes the physical form as Schala's, it stands to reason that he would hand over the Shard if he should have it. Either to free her or at her request.

Schrodinger is made of Narrativium.
The non-flashback portions of the comic imply that Alex did, in fact, face the Sovereign, somehow stopped/stalled her, and is established as the Gamemaster (something Ryan wants to take from him). Schrodinger, in the flashbacks, is running around dropping monkey wrenches (or should that be "kitty wrenches"?) in the plots that could potentially distract Alex from his main objective; in the "present", he's apparently trying to break Alex and the others out. In short, he conveniently irons out minor wrinkles that Alex would otherwise have to deal with, running interference. If you don't think of Schrodinger as a benevolent protagonist, then think of Schrodinger as the stereotypical cat: happy to do what it takes to make you do what it wants.

Colors and emotions are connected in Videoland, similarly to Green Lantern
Princess Hope cast a spell which seemed to have something to do with colors; first she was engulfed in Cyan, Magenta and Yellow, then Red, Blue and Green. The second set of colors are the primary colors which make up all images, including sprites. One of them is Green, the color of Hope. The others are Blue and Red, which when combined, form Purple, the color of Sorrow.
 * Technically, red and blue form magenta in the additive color wheel. Still close enough.

Omega Energy comes from growing up
What happens when you become a teenager? You start getting angsty, and you also stop playing with your old toys. How do you kill a fictional character? By forgetting about them. The inhabitants of Videoland are facing the same dilemma as the toys in Toy Story 3: they're disappearing because one of Alex's older relatives (Kevin?) isn't playing them any more.

The magic words for the Mystic Mouse are...
"Sweet Christmas, that's stupid fresh!" Notice that he hasn't said that for a long time!

We, the readers, are actually part of the webcomic.
The reason why Ryan gets everything totally backward as mentioned in episodes #454 and #455 is so that Alex will end up explaining it all to him and, in turn, to us as well. This is so that all the readers understand everything that's going on in all the different games (especially the ones that particular reader never played). Videoland is actually aware of the existence of the readers and is making Ryan misunderstand everything so that they can follow what's going on, which means our very presence as readers is part of the story.

Schrodinger is evil and somehow manipulating Alex.
Second to last panel, Schrodinger's heaven, that is all.
 * That's a guest comic, and could simply mean he's capricious rather than malevolent.

The Little Girl in FF 6 has the Shard of Tears!
In the flashback where Ryadia meets Bob and after she wakes up, we see that Bob has lost the Shard of Tears and states that a little girl had taken it and gone through the portal. The Little Girl we see in FF 6 has no knowledge or understanding of the world she is in and knew nothing of Kefka or magic. Also, she is clearly Touched, likely due to her contact with the Shard. When she, in turn, caused Celes to be Touched, Celes's focus went to a memory of the past, clearly an aspect of the Shard instead of the Mask.

Locke will end up transported to the battle Cecil is trapped in!
What better teamup can we have than two guys who have lost their wives to the control of the Sovereign? Besides, Cecil's been stuck in that battle since 2003. Who better than Locke to come in and free him, and finally allow for an explanation from the paladin about his part in everything and how he knew to prepare for Alex's coming.

King Charles is The Watcher in league with Bob.
We don't know that he's dead except for Kevin's word, and there's something fishy about how he's been acting. Spoony stated that the Watcher has been "trapped in his glass prison since the golden age of Videoland", and that he is unable to communicate unless someone seeks him out. Who else around that time was noted to have been imprisoned anywhere, and would likely be able to see what's going on in Videoland, even if he's unable to actively do anything about it?

Alex is going to absorb the Sovereign into himself
All of the trouble started when Omega energy was introduced to Videoland by extracting it from a denizen of the Real World; if the Sovereign isn't made of Omega energy entirely, she's got to be composed mostly of the stuff. Thus, the solution isn't to kill her, since that's a real-world solution, or seal her away, since that never lasts, but to return her (or, the part of her being that is Omega energy, depending) to the place from whence her power and essence came- a human being. Thus, why Alex told his Captor that she "wasn't dead" but "wouldn't be hurting anyone ever again", and why he's so much more introspective in the present.
 * A corollary is that this is what the Inner Evils want to kill Alex to prevent; they know that while its the only way to get rid of the Sovereign, it probably isn't going to be very good for Alex's well-being, though obviously not as bad for him as it is for somebody that isn't made to contain Omega energy in the first place.

The Reality Warper child that showed up in the arc that introduced Final Fantasy VI characters...
...is the same child that was mentioned by Wily in episode 681.

Admittedly, the evidence for this is pretty weak: in episode 768 Alex called her "the child", thus using the same expression that Wily used in episode 681.