Stargate Atlantis/WMG

The so-called Lanteans of Stargate Atlantis are not the original builders of the Gate network.
Draga, the winged lizard-like alien discovered in Stargate Infinity, is not remotely humanoid, but is called an "Ancient". This is not because Infinity was deprecated by Atlantis. No, in the decades between the two shows, the name was simply reassigned to a new unknown, and presumably more fundamental, race.
 * The remnant Ancient technology encountered by the SGC has appeared to follow multiple aesthetics, some of them seemingly incompatible with the very-human survivors of the Lantean warship Tria. This is because Lantean civilization lasted for several million years, and underwent many ups and downs and technological cul-de-sacs.

Pegasus Stargates cause brain damage.
The characters on Atlantis often seem to be a few sandwiches short of a picnic. This especially applies to Ronon, who spent seven years constantly traveling from world to world. The only exception is Caldwell, who has his own starship and almost never uses a Stargate.
 * Despite having brilliant scientists, it seems like the Expedition can't so much as turn on an Atlantean iPod without someone losing an eye.
 * That was because the Atlanteans never built an iPod that didn't poke out people's eyes. Of course, the Ancients probably used stargates all the time.
 * Warning: Gate travel may be hazardous to your health.

Pegasus Stargates infect people with Pegasus Logic
This is, naturally, morally superior to Earth logic.

Whenever a Hero is captured, the Others come up with a rescue plan. Caldwell is treated as the bad guy because he doesn't want to sacrifice his thousand Red Shirts and the ONLY Tauri ship in the Galaxy just to rescue one man.

But Pegasus Logic works in its own galaxy. Hero always gets rescued, and it doesn't matter how many Red Shirts die.

Dr. Keller is a Wraith.
On Atlantis, first we see Ellia, a Wraith raised by a human who desperately wants to become human herself. She apparently dies. Then we see the Atlantis crew transform a Wraith into a human, amnesiac but with a complete life story made up by the crew. Then we see a new doctor appear on Atlantis that we've never seen before, who looks exactly like a human version of Ellia. Hmm.
 * That also suggests that Halling, the leader of the Athosians, is also secretly Todd, the leader of the Wraith.

Amelia Banks is a Replicator.
In the episode Lifeline, we see a female Replicator technician. By Quarantine, an identical woman is employed in a similar capacity on Atlantis. Coincidence, or Replicator infiltration?

Michael is the Wraith scientist who gave Teyla and the Athosians Wraith DNA hundreds of years ago
Crossing species together seems to have become Micheal's major M.O., and he's especially interested in Teyla and her baby. He's established to be a brilliant biological scientist, and being a Wraith he could easily be old enough to have been around back then. The fact he's never brought it up in conversation can be chalked up to the memory wipe the Atlantis team gave him when they experimented on him.

Todd is the Wraith scientist who gave Teyla and the Athosians Wraith DNA hundreds of years ago
Michael didn't show any interest in genetic engineering until he was himself a victim of it, while Todd on the other hand seems one of the oldest and most reasonable Wraith in the Galaxy. Not to mention he's also a scientist who has fluctuating standing within the Hive. By making feeding more efficient, he was going to solve the problems he's been trying to solve in Season 5. It would also explain his clear interest in Teyla, and knowledge about her abilities (Episode: The Queen).
 * And was punished for his experiments by being handed over to the Genii.
 * Brilliant! It fits so well. It always pissed me off that Humans treat Todd like Gryffindors treat Slytherins, but, Todd keeps coming back for more!
 * Why don't Wraith have names? How can the Queen order wraiths to work the darts, the artillery, the engines, the shields etc. They could have Handwaved it with puny mortals can't speak wraith.

The Wraith's Villain Decay is a result of the food shortage.
With fewer humans around to feed on, they aren't getting enough nourishment to maintain their Healing Factor that made them so hard to kill in the first place. The link between feeding and Healing Factor is demonstrated in Todd's introductory episode. During the escape sequence, the Wraith that will eventually be known as Todd acts as a bullet sponge. He feeds more than any single Wraith we've ever seen, going so far as to drain Sheppard repeatedly, despite draining to death at least one Genii from every squad they encountered.
 * I do believe this is canon.

Martin Gero and David Hewlett are the same person.
They're both Canadians who have written and directed their own movies, and Gero seems to identify strongly with the character Hewlett plays. They even look reasonably similar - any differences could just be make-up and hair styling. Yes, we've seen them together on a parody video, but we've also seen Hewlett play two characters in the same scene.

Todd is suffering from PTS/Stockholm Syndrome.
Is it a coincidence that the only Tau'ri-sympathetic Wraith character so far was imprisoned for X number of years by humans beforehand? Either he's very forgiving (never seen to be a Wraith trait), or there's some serious mental trauma going on under that mop of his.

Halling is Todd in disguise
In a similar vein to the 'Dr. Keller is a Wraith' and 'Todd gave the Athosians their Wraith DNA' WMG's above, Halling is in fact Todd in disguise. After all, what sort of scientist wouldn't want to monitor his experiment? He's just using makeup like the Wraith we see on Earth in Vegas to look like he's not a Wraith at all.

Ronon is part Nietzchien
Ronon looks awfully similar to Tyr Anasazi. Both of which are physically superior and have advanced fighting skills. Explains how Ronon can face dangerous adversaries like gouald, wraith, hybrids and Tealc.

The wraith are actually the same species as Morbius the living vampire
Its never fully explains how the iratus bug evolved into the wraith and neither does it make a whole lot of sense seeing as their should be all sorts of iratus hybrids. Its well known those lazy ancients are responsible so it was probably a whole host of chimera experiments designed to make a life form either more resistant to the plague or diagonal on the human evolution chain. A lot of radiation and bat DNA mixed with the magic ingredient if Iratus DNA and hey presto- wraith.

Rodney is Decade
He destroyed worlds, uninhabited, but still worlds and he travels to various worlds. He just hasn't discovered the Decade Driver yet.

Had the show not been canceled, Todd would have become a regular.
The original Season Five finale did not have a direct threat to Earth, but rather had Kenny attacking Atlantis after overthrowing Todd. After destroying Kenny's fleet, Todd would have had nowhere else to go. He would have undergone Keller's gene therapy and ended up on Sheppard's team.
 * Todd had already undergone the gene therapy before the end of the show, in the episode where one of his hive ships has a tumor that causes it to tear itself apart. But yeah, they were really hinting at the fact that in season six Todd would be a regular. Oh, What Could Have Been...

Genghis Khan had the ATA gene
It's been theorized that because Genghis Khan got so much action, approximately one percent of earth's population is descended from him. If memory serves, that's about the same as the percentage of people who have the ATA gene.
 * Genghis Khan was an Ancient!

"Home" was the last actual episode
The rest of the series was just an illusion created by those energy beings.
 * Rodney said it himself, "How do we know this isn't a double fakeout?"

"Progeny" was the last actual episode
They are still in a holding cell on Asuras, being mind-probed.

Carson used to be a drug addict
When Rodney is going through withdrawal he states "you have no idea of the agony I'm going through." Carson replies "Oh, I have an inkling." I don't think this was ever referenced again.

Rodney's allergy to citrus came from a bad experience and has no allergy
Alternate timeline, and much happier, Rodney does love lemon chicken, whereas main timeline, and very unhappy, Rodney is afraid of a lemon

Scotland has become an independent country in the Stargate Verse timeline by the time Atlantis begins.
Carson Beckett, the only Scot we see on the base, is wearing a Scottish flag patch rather than the UK flag patch you'd logically expect him to be wearing - unless Scotland is no longer part of the United Kingdom. Otherwise, him wearing that patch makes about as much sense as an American team member wearing their state's flag as a patch, or a Canadian wearing the flag of their home province. It's even relatively plausible, considering the fact that the Scottish independence movement is a very real thing.
 * Scots can be very independent-minded, it wouldn't be surprising at all if he had some Scotland flag patches made for himself to wear instead of the UK ones, and damn the regs.

The unidentified gay male supporting character is Major Lorne.
Just a hunch.

Mensa is aware of the Atlantis Chapter of Mensa
It's a shame they can't host an RG, though, due to the secrecy. All that open space for a convention.