Honestly, I haven't seen that many, and I get dissapointed trying to watch them on tv--so now I'm renting them. In the meantime, I'll have to go with Ghost in the Shell, both the movie and the "Stand Alone Complex."
I do agree that from what I've seen it's a hard choice. Other anime series I've had a taste of include Full Metal Alchemist, Trigun, Blood+ (okay, exactly one episode), Trinity Blood, Inu-Yasha, Bleach, One Piece--there may be a few more I can't think of off-hand. I've seen a few other movies, too, such as A Wind Called Amnesia, Akira, Spirited Away, and couple of Inu-Yasha. There's one or two more for which I can't remember the titles. Okay, yeah, I've seen a couple of Cowboy Bepop, Tenchi and Outlaw Star as well. Sheesh, I've seen more than I thought I had! Anyway, I've enjoyed most of them immensely and it's hard to choose one that's the best.