[9] Title from a Pink Floyd song, which might strike some readers as odd unless they take a look at the lyrics: "Welcome, my son / Welcome to the machine / Where have you been? / It's all right, we know where you've been."[517] Early on, there were many who wouldn't have taken this remark as if it were meant to be ironic - but it would've been all along.
[628] FEISAR (Federal European Industrial Science and Research) is one of the companies that backs an antigravity racing team in the WipeOut games.
[710] If memory serves, Asuka's mother hanged herself.
[721] Ernest Hemingway, A Farewell to Arms (1929).
[806] An original character who quickly became one of our favorites, Kaori Yamashita was envisioned as the SEELE opposite number to both Ritsuko and Maya, though she's actually Ritsuko's mother's age.
[899] Habbalah, being fallen Elohim, are all about exploiting the emotional weaknesses of others.
[1077] Lilith, the computer, is named after Lilith, the mythological figure whom some claim was the first human woman made (and who, in In Nomine, went on to become a demon princess). SEELE will have their little jokes.
[1081] Because, unlike most SAL 9000 systems', Lilith's voice is based on Yui Ikari's, not Naoko Akagi's. Shinji recognizes that on a subconscious level, at least.
[1159] Good little actress, isn't she? But then, she has to be. You don't survive long as part of a cadre like the one Ichi belongs to if you can't play a role.
[1278] Truss and I named all the incidental NERV Security people after people who were pitching for the Red Sox at the time.
[1563] Misato unthinkingly quotes the musical Chess.
[1680] Asuka's facial scar is similar to that sported by the Street Fighter II character Cammy, though it's on the other side. No real reason for that; I just thought it made for a good memento of her experience.
[1700] As seen in the Half-Life games.
[2118] Malphas is named for one of the princes of Hell - in In Nomine terms, the Demon Prince of Factions, responsible for sectarian divisions that tear groups and places apart from within. Another example of SEELE's warped sense of institutional humor.
[2349] The joke here, if you didn't know, was that in Japan, Rei Ayanami and Lina Inverse had the same voice actress.
[2567] Conceptually, it's probably the weirdest of our fake crossovers, but I'll always have a special place in my heart for Batman: Neon Genesis. The concepts involved dovetail shockingly well.