Read or Die/WMG

In the OVA, what Ikkyu is actually going to play is Neon Genesis Evangelion Episode 24.
The Ode To Joy was just a sign of the angst and depression that is to come. Well, there should at least be one theory connecting it to Eva.
 * And Evangelion has its own I-jin clone of Ludwig Van Beethoven, named Kaworu Nagisa.

The Amnesiac Nancy from the TV series isn't the previously evil clone, but the "Good" Miss Deep.
There was no way for Good Miss Deep to know that her "little sister" had brain damage and wouldn't try to kill Yomiko, yet she requested Yomiko to "take care of her." The whole thing was a Xanatos Roulette; Miss Deep knew why the British Library wanted an Ijin body and mind, so she purposely made her brain "unavailable." Pretending to be the other clone was to protect Yomiko as much as possible.
 * What she didn't realize at the time, though, was that she was pregnant.
 * This makes a great deal of sense. Since we don't know how soon Miss Deep joined the British Library after her relationship with Ikkyu, she might not have been pregnant for long enough to realize. As for her staying behind on the rocket as Ikkyu died, she could have phased out and fallen into the ocean without Yomiko noticing. Then again, Miss Deep could have guessed that her "sister" was going to develop amnesia as a result of air deprivation; but that's an even greater stretch; when you think about it.

The Gentleman Lives!
His mind has now been divided between Junior, Anita, and Joker. The dog in the ending of RODTV was a psychic message to awaken Joker from Gentleman's essence floating about in the atmosphere. Anita and Junior have their free will, Joker probably doesn't.
 * What about Nenene with 17% of the Dokusensha Perfect Language in her head? Will that activate similarly?

Yomiko is a Contractor
She has all the traits common with contractors from Darker Than Black. Her ability, obviously, is her control of paper, and her renumeration is reading books. The I-jin were actually clones of historical figures, but exposure to Hell's gate mutated them, giving them various special powers, but mutating some of them (which is why the glider guy is blind, Beethoven has the tubes running to him, and the fire-breathing Buddhist has an artificial heart.) Junior's tracking device included a localized artificial copy of the meteor fragment, drawing out his inherited powers when it was active, but deactivating when it was removed.

Anita is the Final Book of the Gentleman, given human form.
Yes, it's a little late to be giving this one, after the series is over and the actual plot Jossed this quite thoroughly; but this was This Troper's theory at the time.
 * Anita is a Paper-User...yet hates books. Her Power must come from a different source than the others.
 * Maggie and Michelle met Anita on a mission looking for a Gentleman Book for Dokusensha. Yet it wasn't at the location they were told. What they did find was Anita.
 * They weren't actually looking for a Gentleman Book, they were supposed to verify the authenticity of the books in the basement. But it's still a cool idea.

The Gentleman is an Alternate Universe version of The God-Emperor of Mankind.

 * Built a legendary empire? Yes. Able to change time and space? Yes. Dying/Dead and his followers are going through some very extraordinary steps to keep him around? Ding ding ding!

The Gentleman's Final Death warped space, time, and literature.
As the British Library were about to resurrect The Gentleman; his powers were pushing London back in time, and bringing stories to life. After the Resurrection was stopped, his power mingled with the entire world. It wasn't enough to bring about Instrumentality, but books became Serious Business to everybody, London remains a magical and scientifically advanced dictatorship, and anyone with the right kind of will can walk into or out of stories.
 * coughs:

There is a set of "copies" to the Gentleman Books.
The Fantasy Library from the Read Or Dream manga, copies of every book ever made; even ones that used to be people. In Ten Years, Joker will send agents to check out each book and give up his own mind for the Gentleman. Ordinarily, this would be impossible for a normal human; but having a partial amount of the Gentleman's essence for 10 years made him a suitable host.
 * So much for being an Alternate Universe!
 * EXCEPT... the Fantasy Library showed up every 10 years in the SAME PLACE. Hong Kong. Which is now half-sunk underwater. So while this is still plausible, it would be a heck of an effort to recover it.

Readman is a bibliomancer
Her obsession with books fuels her powers. It makes sense, in a wacky sort of way.
 * So, if I read more books, will I get paper master powers?
 * It's doubtful, but not impossible. This troper has been reading since he was three years old and no special abilities have yet come of it.

ROD takes place in the same canon as The Venture Brothers
I say this simply because The Guild of Calamitous Intent is run by a guy who occasionally associates with The British Library (under a carefully-made alias of course) - "Jiggy Stardust"

Yomiko is Anita's mother
Anita was created artificially using DNA samples taken from Paper Masters in the employ of the British Library. Two people who meet this criteria at the time this happened are Yomiko Readman and her mentor/lover/predecessor, Donny Nakajima.

The British Library is essentially the Illuminati
this may seem obvious, but the British Library is a shadowy secret organization controlled by the The Gentleman with plans to take over the world, their plan near the end of R.O.D The TV is pretty much the "New World Order" of various conspiracy theories
 * It seems that the British Library is actually Seele, with the Instrumentality plots and all.