Anime theme song... hm, there are so many I like but I'll have to go for the "most".
Hare Hare Yukai. The ending theme song for Suzumiya Haruhi no Yuuutsu. It definitely fitted in that anime series very well. And it is easily identifiable to the Haruhi anime series when you hear it play.
On a side note, if you heard Minoru Shiraishi's version of that song, I will not blame you if you don't like Hare Hare Yukai.
Shiki no Uta, the opening theme to Last Exile, and ALL of the music in Hellsing (original) are all topnotch! I think I'll listen to some of them now...