Dragaera/WMG

Vlad will join the Lavodes
Think about it. Sethra wants to bring the group back. She already has Telnan, who says she only picked him up because of his Great Weapon. After a certain comment in Issola from Sethra ("This is the sort of thing Vlad is trained for..."), when you consider that, it seems likely that she'll be using him at the very least as a "Lavode Irregular."
 * It doesn't hurt that if you look back, you'll see that while that comment probably referred to his specific reincarnations (the process isn't at all random), there's a double meaning there: a lot of Vlad's early training in life.
 * This could be another reason Aliera devotes so much of her time to genetic research.

Devera is Haruhi
They're both dark-haired, they're everywhere, and rules of physics/time/space do weird things around them. And it might explain why Haruhi is really-a-god-except-not.

The e'Driens are descended from the house of Kunou
The resemblance between Morrolan e'Drien and Tatewaki Kunou is obvious - they're tall, dark-haired, sword-wielding, ruthless, Sesquipedally Loquacious, and arrogant enough for five aristocrats. Then we have the fact that Drien is said to have changed sex about midway through hir career, suggesting that s/he may in fact have been Ranma. (For details about the temporal mechanics of all this, ask the Necromancer.)

How Kragar got kicked out of the house of Dragon
He himself gives an explanation about not being able to command troops, but it's been noted that in the book Dragon, there are plenty of common Dragon foot soldiers, which makes this explanation somewhat dubious. It's also odd that Aliera seems to have a personal dislike of him, which would suggest he was someone she knew before the events of Five Hundred Years After, but this doesn't seem to fit the chronology. I know one theory is that he is actually a half-breed, since as noted, that seems to get you kicked out of the House, whereas evil deeds rarely seem to. Personally, I wonder if he acted in cowardice on the battlefield and got tons of troops slaughtered because of this. Another explanation might have something to do with the Jhereg-Dragon war, but seeing how Mario and Kragar are allies, it doesn't seem likely they were on opposite sides in this.

Vlad will destroy the Cycle
May have been foreshadowed in Taltos. And can you think of any better Crowning Moment of Awesome on which to end the series?
 * That seems to fit with Brust's political views.
 * While definitely a nice thought, it's probably ruled out by the fact that the Paarfli books are "written" after the Vlad series and the Cycle is alive and well (although you do get the impression that things are a bit more equitable by then- which is why there's some much emphasis on the "good old days")
 * Alternately, Zerika might subvert the expected course of the Cycle by abdicating as Empress, then -- since she'll no longer have her hands tied by imperial politics -- unilaterally throw open the House of the Phoenix to Easterners. As the sole member of her House, she'd have as much right to decide this as the Jhereg Council ever did, and she's already mentioned that abdication is a reborn Phoenix's means of remaining reborn, not decadent. So her bestowal of an Imperial title to Vlad would be foreshadowing for a much greater shift in Easterners' status within the Empire, that would simultaneously save her House from extinction and make reparations for how she'd had to repress Easterners during her reign.

Vlad is still/again Aliera's brother
Verra is awfully tolerant of his snarkiness. Near the end of Phoenix, when he tells her he doesn't want anything more to do with her, the goddess replies, "I won't hold you to that. You don't even know who you are yet." Vlad has little or no memory of his mother, and his father seldom if ever talked about her. Aliera, of course, has no idea of this, and it'll shock her every bit as much as it will Vlad. Devera knows, naturally. Sethra might suspect.
 * Also, this is why Vlad is able to leave the Paths of the Dead in Taltos. It's got nothing to do with him being an Easterner; it's because his blood, too, is the blood of a god.

Kragar is Mario's son
Mario is Dragarea's greatest assassin, and having a skill like near-invisibility would go a long way to explaining how he got so good. Plus, it was revealed that Kragar is Mario's contact person, and who would Mario trust more than his own son?
 * That would go well with the "half-breed" theory and also explain why Aliera hates Kragar so much.
 * This troper officially subscribes to this theory! It all fits, and doesn't have the age problem of the theory that says Kragar IS Mario.

The Vallabar Paarfi knows is Vlad
On the surface, the Paarfi books give the impression that Vlad didn't really accomplish anything/ the Cycle hasn't really changed, and Paarfli certainly never mentions Vlad by name. However, I just had the theory that like Lazlo (think that's the right name), Vlad will be one of those humans who has enough magic power to have a lifespan comparable to a Dragon. And owning that restaurant would probably be his favorite choice if he's ever allowed a peaceful retirement.
 * At least partially jossed by Tiassa, which includes portions where Paarfi writes about Vlad himself, although this might still be possible down the road.

All Great Weapons contain Dragaeran Souls
Not sure if this was ever explicit, but I've come across this argument elsewhere. Drien, as noted above, was a Gender Bender, and Morrolan's Great Weapon is of ambiguously gendered. And, Godslayer and Aliera's soul pre-resurrection show how souls can be used to form this weapon type. A related theory I've come across is the idea that Telnan's sword contains Tazendra's soul, given their similarity in personality- and it would also explain how Sethra found him/why she took him on, since Tazendra was a Lavode.
 * Morrolan's Great Weapon is Blackwand, who is distinctly female. Pathfinder is ambiguous. I do like the idea that "Nightstalker" is Tazendra, but I don't recall if she was killed with a morganti weapon, which from the admittedly limited evidence, would seem to be a requirement
 * Tazendra was killed by grievous wounds inflicted by sorcery. Though the possibility exists that being in single combat with a Jenoine at the time would affect that sort of thing, neither the narrative nor Sethra, who probably would have the best guess out of anyone, give any hint that her soul was affected by all of this. She was at least commended to Deathgate, which generally requires a soul to accomplish. I personally prefer the theory that Telnan is Tazendra reincarnated.

Related to the guess above, Loraan (you remember him, from Taltos) was trying to make
Think about it (end of Issola spoiler)  Sorry about the huge spoiler, but... it is a huge spoiler! Still, there's nothing against it!!

The blood in the vial was Vlad's
Vlad is destined for greatness (or at least usefulness) and it would be a real Mind Screw.
 * To explain this a little further, Vlad will at some point ascend to become a god. Verra and Sethra planed for this to happen and gave him his own blood to help Morrolan. He wasn't allowed to leave the paths of the dead because he was an easterner, but because he will be at some point be one of the gods. Vlad can't remember because of Verras manipulations of his memories.

Vlad is the great-grandson of Zerika and the Warlock
My guess is that Zerika and the Warlock had a child, which is either Noish-pa, his wife or one of the parents of Vlads mother. Because of this bloodconnection Vlad was able to be born with a soul that was previosly in a dragaeraen (is that the right word?) body. It is never stated that both species can't have children and even then the Warlock could have tried some witchcraft or Sethra, Verra or one of the other gods could have intervened to save the House of the Phoenix.
 * Aliera does say that Dragaerans and Easterners can't interbreed, when she explains the origins of the Houses to Vlad in Jhereg.

Vlad is a Brain in a Vat
The reason he could leave the Paths of the Dead is never fully explained, so perhaps he never did. Sometime while he was in the Paths, Vlad was brought between the "real" world and a simulation. His entire life after leaving the Paths has been a lie crafted carefully to basically keep him occupied. While replicating reality somewhat, this world is tailor-made for Vlad, explaining some improbable coincidences later in his life.

One of the extinct original tribes of Dragaerans was the Tribe of the Norska.
The Tribe of the Dragon wiped them out in instinctive self-defense, because norska eat dragons.

The House of the Yendi doesn't actually exist as a distinct bloodline.
The original Tribe of Yendi died out thousands of years ago, or perhaps never existed in the first place. Rather, the Yendi arose because various Manipulative Bastard members of other Houses/Tribes collectively conned their way into a place in the Cycle, adopting alternate identities as "Yendi" and establishing the ruse of an additional House. The Sorceress in Green looks like an Athyra because she is an Athyra, albeit an extra-sneaky one who opted to forsake her birth House to live as a "Yendi". Those "Yendi" who have no distinctive House features, such as Pel, are cross-breed descendents of such hoaxers. Any reputed "Yendi genes" that someone like Aliera might search for are merely normal genes for being a Magnificent Bastard, not Jenoine-imbued snake genes.

This makes it easier to explain how a House with as little overt authority as the so-called "Yendi" could seize power when their turn of the Cycle comes up: they don't. They just wait for a Chreotha who's sufficiently sneaky to meet their standards cons his or her way onto the throne, then "out" them as a "Yendi" and claim the accolades for having the Cycle turn in their "House's" favor. Likewise, the House of the Orca take power when an Orca who leads an alternate life as a "Yendi" maneuvers his or herself into position to claim the Orb, then admits to being an Orca and declares the Cycle to have turned, the better to profit financially from an Orca administration.