Star Trek Online/WMG

Several events depicted in previous Trek shows will occur in-game
2409 is pretty much the perfect time to have a lot of these things happen.
 * We'll help Janeway go back in time again to complete the time loop (she's a bit late this time, after hesitating, but she realizes if she doesn't Voyager and the universe are boned.)
 * The fun gameplay bit coming from the fact that the tech she needs is Klingon, and, well, that's just a hair problematic now.
 * Worf will die on the floor of the High Council, as per the TNG episode, either in backstory or in a game event.
 * One might assume he is already dead, as he would surely have been one of the most vocal opponents to open hostilities with the Federation. Although he wasn't exactly what you could call friendly in "All Good Things", that probably had more to do with Troi's death and he and Riker's unresolved feelings on the matter. One does look forwards to seeing a Future Badass Alexander though, who is willing to break all sorts of rules, that are in place for very important reasons, for people he cares about. What would that mean for Mom and Pop back on earth? (If they're still alive, that is.)
 * Worf is dead, and has been replaced by an Undine?
 * Actually, in the recent Season 2 content update, the Klingon Episodes feature an elder Worf alive and well as an adviser to house Martok. He appears to be dedicated to preserving house Martok, and does not appear to have been replaced yet. As far as I've seen, thus-far this is his only appearance, and perhaps we may well seen his prophesied death in-game.
 * We'll run into Captain Harry Kim aboard the Rhode Island (the Nova-class is available to players, to boot!)
 * Nog may be a captain by this point.
 * Jake Sisko's novel Anslem may well be published during or immediately before the game starts.

The Guardian of Forever will be used to show us a ton of events from the shows
There are videos out there already of it showing scenes from TOS and Generations; we'll probably get to help beat Soran or meet Zephram Cochrane.

STO will explain exactly why the Romulans seem to have all the same names and whatnot as the Roman civilization on Earth.
Oh, man. If that's not a hint, what is?

Admiral Quinn is
Let's see, Suspicious? Nawwwwww...
 * Man, first he's infested with neck parasites back in TNG, and now this. When it rains, it fucking pours.
 * This is a theory I kept coming back to. Hes gotta be working with someone.

Jean-Luc Picard's
One Mission in the Task Force Hippocrates Quest

Everything is an Undine plot.
This is made by Cryptic, after all. And since they are perfect shape-shifters, it only makes sense that they're everywhere in the higher ranks!
 * Actually pretty jossed.

The Federation has absurdly high standards for Starfleet.
Starfleet requires officer-training for postings that would be mere enlisted in an ordinary navy, and even then only takes in the very best of the best. This explains why the Federation is strapped enough for manpower that an ensign can be put in command of a ship (the Federation has been doing this for too long to let go of their standards easily), and how a mere ensign can be qualified to be put in command of a ship. This could be because of Starfleet beginning as the best-of-the-best working together in the early days of Coalition/Federation, when the various members still had their own navies as well.

The Dominion will return
Sure, they may have gotten kicked in the teeth at the end of Deep Space Nine, but with this much chaos abounding, you can't really believe they'll stay in their pudding planet for long.
 * confirmed

The reward for completing the Dominion featured series arc will be a Jem'Hadar Bridge Officer
Ketracel White can't just be there for replicator trash, right?
 * As of the fourth episode of the arc, released 3/3/2012,

If/when Star Trek returns to television, it will follow the basic plot of STO
It seems likely that the franchise is going to come back to TV sometime in the future, given the popularity of the most recent film. Since there's so much more 'official' involvement in the game then there has been for any Expanded Universe material, could it be possible that the Powers That Be are using Star Trek Online as a testing ground for new TV series ideas? That would be awesome.

B'Vat went on a long-term mission at some point.
As in The Emissary. It would explain the Fridge Logic in him being.

The Iconians weren't bombed for being bastards.

 * They were a standard Precursor Race but then got nuked halfway into oblivion. 200'000 years later, they're still a little sore.
 * Alternatively, 200'000 years is a long time for things to change and people to get over things. An imperialistic Iconian government has arisen to power in the interim, and now they are getting involved in the galaxy for their own reasons. They're just using a tech advantage garnered from 200'000 years of space-faring history.

The Iconians haven't really come back. It's all a plot by the Tal Shiar, who have access to Iconian science and technology.
Notice that we have never directly seen or interacted with an Iconian in the game and neither have any of the NPCs, including people that should have. The only hints that the Iconians control the Tal Shiar come from people like Obisek, leader of the Reman resistance, who have no firsthand, direct knowledge.

The "Iconians" also captured Empress Sela, a known enemy of the Tal Shiar who attempted to assassinate the head of the order...a kidnapping done with Romulan ships and equipment. Why is it necessary to assume an alien force made the Tal Shiar capture someone who is already their enemy?

In addition, in the "Countdown" comics, it was established the Romulans are hungry for revenge after the supernova, and their modus operandi for this revenge is to reverse-engineer captured technology from more advanced alien races, like the Borg technology to create Nero's ship, the Narada.

The Iconians as malevolent ancient conquerors contradicts what we've learned about them from the episodes, which presented them as a scientifically advanced culture destroyed by less advanced races who feared them for their science. The TV episodes featuring the Iconians like "Contagion" strongly hinted that they were never conquerors. Zero evidence is presented for the view they were warlike, as, Picard himself pointed out, no Iconian weapons were ever discovered: the only known Iconian "weapon" is a probe that disrupts computers, though even that, disrupting computers, might be an accident without malevolent intent.

Picard speculated that the Iconians were not malevolent or warlike, but were feared and misunderstood by less technologically advanced races. If they really were aggressive conquerors, would less advanced races have really destroyed their homeworld?