WMG / The Elder Scrolls IV: Oblivion

Hannibal Traven has been to the Soul Cairn
Which is why he has such a hatred for necromancy because he knows first hand what happens to people who are soul trapped into Black Soul Gems. Also, of course how he escaped could possibly be Authority Equals Asskicking. And how he got there in the first place may be that he was once a Necromancer himself and is trying to atone.

The loading screen quote about turning off always run in battle was put in in the hope that players wouldn't discover how easy it is to dodge.

The Bruma Mages' Guild hall specializes in alchemy.
The other six guild halls specialize in a specific type of spell. There are seven magic skills, six of which correspond to specific groups of spells. The reason that the people who sell spells in Bruma don't have one specific group of spell available is because they don't specialize in spellcasting. Instead, they specialize in making potions.

The hero was falsely imprisoned or framed
The hero specifically asked Uriel "Why am I in prison?" which gives the implication s/he did nothing wrong at all. Or more likely, Uriel being the seer that he seems to be, purposely (secretly) ordered the hero to be arrested and placed in that cell to fulfill the prophecy.

The Dark Brotherhood killed Count Indarys' wife.
People in-universe and out always seem to blame the Count for his wife's mysterious death because he's apparently a scumbag. However, when you take into account the rumor that the Dark Brotherhood bribes said Count to keep his mouth shut about the existence of the Cheydinhal sanctuary (the exact words used are "bribes and other... incentives"), it could be possible that at one point he tried to do something about them, and they killed his wife to teach him a lesson. Because of his reputation, or maybe just because people are prejudiced against a Dunmer Count, or even because of the Brotherhood themselves spreading rumors, everyone just blamed Indarys for his wife's death and decided not to look any further into it.

The Hero is into necrophilia.
He or she knows the penalty for grave-robbing is death without being told beforehand and is able to rattle off the fine for necrophilia. Sounds like things someone would want to know if they were into dead bodies.

Mankar Camoran is somewhere or other in his ancestry an illegitimate child of a Septim or something
It explains how the hell he can wear the Amulet of Kings without issue.

Skyrim gives another possible explanation. All previous wearers of the Amulet of Kings were Dragonborn (Alessia, the Remans, Tiber Septim and his line). Before Skyrim, these folks had all been humans, either Nords or Imperials, and thus possibly related. As of Skyrim, a Dragonborn can be a member of any sentient race, so there's nothing stopping Mankar Camoran as an Altmer from being Dragonborn. Ironically, even though the creators weren't thinking of it, I think it actually explains Camoran better than anything that was present at the time of Oblivion.
  • From his own Commentaries on the Mysterium Xarxes: "Offering myself to that daybreak allowed the girdle of grace to contain me. When my voice returned, it spoke with another tongue. After three nights I could speak fire." Three days is far too short for a non-Dragonborn to learn the Thu'um. The Greybeards spend years training to understand enough to use the Thu'um. But unless "speak fire" is metaphorical, and given how the rest of the Commentaries are written that's a definite possibility, all it would have taken is for the Mysterium Xarxes to have the construction of a Word Wall on the pages we didn't see, but that only works if Camoran was Dragonborn.
  • Technically the history of the Empire implies that there was a Dunmer wearer, in that the Amulet of Kings is part of the Imperial regalia, and Katariah did reign in her own right for forty-seven (or forty-six, depending on the source) years. It is possible she just never wore it (the whole 'already having been Regent for a while' thing smoothing over the transition with the Elder Council) or used it to light the Dragonfires (that being less pressing at the time with two more Towers up and active), of course.

Mankar Camoran is an Ayleid
Most Altmer follow Auriel (although there are exceptions), but most Ayleids were Daedra worshippers (they worshipped Auriel too, but still). Mankar's Paradise has Ayleid architecture. He even loves torture as much as they did. And it would explain the need to claim being the son of the Camoran Usurper (because, officially, he would have no parents to speak of, Ayleids being "extinct" and all); alternatively, he is the son of the Camoran Usurper (it would fit his self-alleged cannibalism), but performed nymic surgery to become Ayleid. His offspring is implied to be artificial in some way, and the reason for it could be that no female Ayleid was available to beget the kind of offspring he wanted. Kirkbride's Nu-Mantia Intercept said that Ayleids were coming back, but 200 years after (Skyrim time) they are nowhere to be seen. Mankar could wear the Amulet of Kings because Ayleids were the builders of the White-Gold Tower, and the Amulet contains its Stone. His plan doesn't only fulfill Mehrunes Dagon's wishes, but it also breaks the covenant between the killers of his race and the "false god" Akatosh.

Mogens Wind-Shifter could have been innocent.
Despite the strong hint of But for Me, It Was Tuesday with this quest, we are only shown Mazoga's introduction to the player and her encounter with the bandits. It's quite possible she had targeted the wrong man, by mistaken identity or some other reason.

Lucien Lachance is a cured vampire.
Vicente Valtieri mentions that he joined the Dark Brotherhood two hundred years ago, and that when he first joined, the Sanctuary was controlled by a different Speaker; Lucien assumed the role of Speaker after her death on a mission. Unless said Speaker was a elf, that would have to have been a very long time ago. Not to mention Teinaava says that Lucien raised/trained both him and Ocheeva and that they consider him a father, despite his not appearing that much older than either of them (he looks like he's in his early 30's at most!). Lucien is a former vampire who, for whatever reason, grew tired of vampirism and had himself cured.

Sheogorath's current plan to stop the Greymarch was possibly inspired from the Nerevarine.
Morrowind left plenty of room for interpretation that the Player Character became the Nerevarine through the act of mantling. With the knowledge of what happened being recent and fresh, this gave Sheogorath a Eureka Moment to hopefully combat the Greymarch by having the Player Character of Oblivion take on the mantle of his role while he becomes Jyggalag. Knowing that mantling is outright capable of turning mortals into deities might have given him the idea in the past before failing, but seeing it recently done could have given him an idea of what exactly he had to do to execute the plan.