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.

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.

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 a Time Lord
Because somebody has to be. Besides, there's no way she can afford to own a building in downtown Tokyo just to store books in if she doesn't have some income from some other century, and a lot of her books look to be newer than they should be. Also, she already fits the naming convention: she's The Paper.