Planescape: Torment/WMG

The Nameless One is a facet of the Eternal Champion.
The Planescape setting already features a massive conflict between Law and Chaos (The Blood War), and The Nameless One happens to be a tragic, extremely powerful individual condemned to fight that war for eternity (Or at least, until the Planes die off). The Dungeons & Dragons multiverse could very well be a part of the Multiverse.

The secret to the Nameless One's memory was the invocation of the player.
The incarnation that discovered a means by which the Nameless One's memory could be preserved between deaths was Dangerously Genre Savvy, and hit on the critical importance of the player in determining the outcome of tabletop and video games. He arranged it so that Planescape: Torment would be created in our world, but by the time it was released he had died a few more times, leaving us with the playable incarnation. The reason the memory endures is because the player is there to share the memory. However, the incarnation wasn't the only Dangerously Genre Savvy character wandering around; anyone capable of outright killing the Nameless One has, through madness or transcendancy, mastered the blackest art: that of the Game Over.

The Nameless One's name wasn't Adahn.
It was Adam.
 * That... makes a terrible amount of sense.
 * This may be my favourite theory I've ever read on WMG. To expand on the points in favour: if one assumes the Christian parallels fit, this slots neatly into the First Incarnation's story, as he commits a sin so grave the planes have been dying ever since. As mentioned, the Nameless One always lies that his name is Adahn, and when discovering his name realises that it's a simple thing, and not what he expected - the name Adam being deceptively simple. Further, this puts a new spin on the game's central question: "What can change the nature of a man?" Adam means, essentially, 'man'.
 * And from a bit of a meta perspective, the answer the game essentially gives you (the player) is "your choice." From certain theological perspectives, Adam and Eve chose to exercise their wills and disobey God. This one DOES make a scary and remarkably awesome amount of sense.
 * It makes me wonder what happened to Eve, though.

The Nameless One's name is Torment.
Less brilliant, but like a certain other nameless, centuries-old living myth, the Nameless One might be the origin of the word Torment, it having come to mean what it does only through association with his actions.

The Nameless One's original crime was the instigation of the Blood War.
A crime so massive and downright evil that the planes seem to be slowly dying of it? The Blood War fits the bill well enough. Far back in a time before even surviving myth, the original incarnation instigated the Blood War for fun, profit or an ideal, and ended up causing a tumult that would endure for millenia, killing thousands by the hour. Therefore his ultimate fate: to fight as a soldier in a war of his own making.
 * The problem is that the Blood War has never had much in the way of collateral damage. It's always been contained to the lower planes, and is viewed by most everyone as a positive thing. It keeps the demons and devils occupied so they don't conquer the multiverse.
 * Yeah, the Blood War is a good thing. It keeps the demons and devils fighting each other instead of overrunning the rest of the cosmos.

Branches of the Ravel tree include...
Chris Avellone has said that Ravel's existence spreads through the planes like the branches of a tree. The other incarnations that appear in Planescape echo her existence in small or large ways. Due to the nature of belief on the planes, these incarnations may not start out resembling Ravel, but they come to resemble her in their lifetimes. Here are some from other planes:
 * Icewind Dale: The blind seer and the cat lady of Targos (confirmed by Chris Avellone himself)
 * Dragon Age: Flemeth, an old hermit crone with intense magical powers and extraordinary longevity
 * Fable: Theresa, blind seeress possessed of incredible longevity and arcane magical knowledge
 * Knights of the Old Republic: Kreia, twisted blind seeress possessed of arcane magical knowledge. For bonus points, written by Chris Avellone and imbued with some elements that didn't make it into Ravel's character.
 * Final Fantasy I: Old and insane blind seer, Matoya
 * The Dark Tower: Rhea of the CÃ¶os
 * Vampire: The Masquerade Bloodlines: Pisha the Nagaraja, a flesh eating vampire living underneath an abandoned hospital, with a vast knowledge of magic and the future.
 * Silent Hill: Dahlia Gillespie, evil, demonic witch extraordinaire. Dahlia is probably only just becoming one of Ravel's avatars, and the first hint is her looking ancient while really being only 40.

For about five minutes of the Good Ending, the Nameless One was the most powerful being in the multiverse.
The Nameless One's last acts before he accepted his ultimate fate were to revive his companions, speak with them one last time, and open portals to send them back to Sigil. For those who might not know what this means, the Nameless One created portals to the city where no portals are created without the permission of the Lady of Pain herself. For the brief span of time between joining with the Transcendent One and his descent into the Blood War, the Nameless One could casually ignore Her Serenity and create changes in her city against her will. If he could do that, it's possible he had the power to undo his own punishment... and chose not to.
 * You can cast Gate to go to Sigil any time you like. In fact, you can cast Gate to get out too. It just so happens that most people can't cast ninth-level spells.

The Nameless One is the father of Cyric.
How else could a mere human kill a demigod (Bhaal) unless he had the blood of an immortal coursing through his veins? Yeah, Godsbane helped, but only so much. Considering that several of TNO's incarnations had had a way with the ladies, it's not hard to imagine TNO from getting one (or several) pregnant.
 * Godsbane...the avatar of the god Mask? Helped only so much?

In life, Morte looked exactly like Joe Pantoliano.
Not just because the guy usually plays archetypal traitors and liars, but because of his role in Memento, which, without going into spoilery detail, is broadly similar to Morte's in Planescape. On top of that, they even act and sound similar, with the same outward Deadpan Snarker front.

The Nameless One's sin was creating Coaxmetal
Because I can't think of any worse crime than creating a entity that desires to destroy all universes, and succeeding in many of its attempts. Of course, it has probably forgotten its maker, and now attributes entropy as its creator and commander.
 * After more study of the Planescape setting, I shall elaborate. The Nameless One was formerly a fanatical Doomguard, and created Coaxmetal as the ultimate tool of entropy. However, he abandoned the Doomguard after realising what he had done.

Fell was supposed to be able to join your party
Because it just makes so much sense. All the other party members have their own contradictions (a chaste Succubus, an enslaved Gith, and so on,) and so the idea of a Dabus who has fallen out of favour with the Lady of Pain fits so well. In addition, there seems to be something missing from Fell's Tattoo parlor. He's a guy who knows you, tattoos play a massive part in the game, he's relevant to your back story. Plus he's interesting. Maybe I'm wrong, but I just get this incredible feeling that, at least in one stage of development, they had Fell down as a potential party member.
 * Hell, I'd rather have him as the healer than Fall-From-Grace. I'm totally going to mod him in as a party member.
 * Fell was a canon NPC in the source material, so that might explain why he's so well developed.
 * Specifically, Fell was the first (and so far only) Dabus to worship a god. He chose to become a worshipper of Aoskar. The Lady didn't take that well. At all. That is why Annah is so afraid of him.

The Nameless One's incarnation name for the player character, should the events in the Negative Plane be told from the perspective of the other incarnations, will be The Inquisitive Incarnation
In fact, this aspect of his nature is what allowed him to get so much further than any other incarnation. His power to make people who are about to kill him stop and answer any questions he might have. This is most obviously demonstrated by the demon that accosts you in Curst's underground. He wants to eat you, but he feels compelled to stop and answer your questions first.
 * It also makes sense as far as the fact that he's the only one who can retain his memories goes. His mind has been broken so often that there is nothing left to break, leaving him with an empty mind, brimming with questions and longing to have them answered to fill that empty void that is now his existance.

The Nameless One is Tharizdun.
He isn't chained, he's forgotten who he even is. Explains a lot.
 * Alternatively, going by 4e Points of Light story, The Nameless One is the person who originally made contact with the Obryith lords; he was a follower of Tharizdun and established a link between his god and the original demons, which lead to the shard of evil being forced into the universe, lead to Tharizdun going mad, lead to the creation of the Abyss itself, the primeval war between law and chaos, and eventually the Blood War and now the Abyssal Plague.

Vhailor is an homage to the Tin Woodsman.
He's heartless, he used to be human, and he carries an axe.

The ending is the beginning of the end for the Planes.
Think about it: petitioners retain no memories of their former lives, and petitioners sent to fight in the blood war are incarnated as grotesque creatures like Lemures (see the original campaign setting material if you don't believe me.) When the Nameless One wakes up in the Grey Wastes, he's still in his human body, and his remembrance of Ravel's words suggests he still has his memories. This is a Very Bad Thing since the Nameless One now has the memories and abilities of over a thousand lifetimes. Either side of the war he joins will have a serious advantage, and this may even lead to the end of the Blood War. The campaign setting material makes it very clear that the Blood War is the only thing keeping the Demons and Devil's from attacking other plains. Therefore the Nameless One's reclamation of his mortality ended up dooming all of reality!
 * Ao is really an idiot.
 * Except, depending on your ending, he's not guaranteed to join either side. In the best ending, I expect him to keep being good.

the punishment at the end is entirely voluntary on The Nameless One's part.
OK, this may not seem like much, but upon arriving in the hellish Planes, he picks up a weapon, nods and goes into battle. Sure, it could be a "yeah, that's a neat weapon" nod, or a "OK, let's go kick some ass" nod, but in a story where many little details seem to have real significance, this little gesture suggests that he's making a decision. So he has a choice. Then, just perhaps, The Nameless One has kept his incredible power but, after remembering his past lives, accepts that he has to redeem himself. Note that - as mentioned above - he keeps his human body, that there is a "what can change the nature of man?" voiceover, and that he didn't seem to die before undergoing his belated punishment - it looks like he was pulled bodily into another plane. Hence he probably didn't forget things. And knowledge, like belief, seems to be a very important thing in the Planes. And lastly, but very importantly - why would the Nameless One lose his incredible power? There is nothing that indicates he did.
 * It certainly makes sense to me. After all, how does The Nameless One gain the memory in the bronze sphere? By feeling regret. How can he take full advantage of it? By accepting the regret, accepting all the evil, all the sins, all the pain his existence has caused to the point where he can weaponize it. Honestly, if you went through all that, the only logical conclusion is that he would, upon feeling full and complete regret for all his incarnations' actions, willingly take the punishment upon himself.

Planescape: Torment is a sequel of Baldur's Gate
The Nameless One is the Child of Bhaal if he were a Human male, followed the evil path and chose to remain a mere mortal being. After some times, he began to regret his deeds, and found a way to become immortal, so he would have the time to fix his numerous mistakes. It went horribly wrong...

The Nameless One is the Doctor
Read the full story here.

The Nameless One is Perrine, founder of the Godsmen
Because it would be just like this game if the founder of the Godsmen started that faction based on nothing more than the desperate hope that even someone like him could escape damnation and attain divinity.

Alternatively, The Nameless One founded every faction, or at least every faction he can join during the game
When he saw how the conflict between his factions, each of which was founded with the best intentions, was tearing the planes apart, the Good Incarnation repented of what he had done, and realized that he might need several lifetimes to make up for it. This would also explain why he feels no disconnect in joining any or all of them in a single playthrough.