My three biggies:
Haibane-Renmei
Serial Experiments: Lain
Neon Genesis: Evangelion
Also Outlaw Star (from what I know of Cowboy Bebop, if you like it you'll probably like OS), RahXephon, Fullmetal Alchemist, Melody of Oblivion, FLCL, .hack//SIGN, Saiyuki, Get Backers, Paranoia Agent, also...