Thanatos - A nice dramatic theme I've always enjoyed, used very well during the series in eps 19 and 23. Also enjoy the 2 remixes from End of Eva, the first which occurs during Misato's last scene with Shinji, and the other obviously the lyrical.
Mother is the First Other - Most of the 'psychological scene' themes are rather dull and lifeless but this one has a better, epic feel to it and has a mysterious touch to it. The version with the orchestra used for the EOE trailer is even better, likewise with the 2 remixes in the movie. Very similar to a theme from Ideon's ending.
Seperation Anxiety & Infantile Dependence, Adult Dependency - Two more themes used during the psychological scenes that while not as good as Mother is the First Other are pretty good too.
Jesus Bleibet Meine Freud - I've always loved this piece of music, and that it is in EOE makes it even better! :)
And may as well come in from the other side too, which are the ones you can't stand?

Fly Me to the Moon - I liked this at first, but the umpteen remixes and absurdity with it on the OSTs turned me completely off to it. It would have been nice if they just kept with the original (I mean the first Eva version of it) and nothing else, but that didn't happen.
Likewise, the instrumental remixes of that and Cruel Angel's Thesis are ones I don't particularly care for either.
PLEASE try to mention WHY you like/dislike various themes rather than just posting a list and nothing else :p I'd like to hear other people's opinions on the various music tracks.