I think Cowboy Bebop is so beloved in the west because it has a very western tone to it, as opposed to a purely Japanese mindset that permeates the majority of anime.
I enjoyed Blue Submarine 6, it was kind of like Water World without the suck, but also sans cult appeal.
Has anyone else noticed the striking similarity between Outlaw Star and Firefly? Both start with a girl with a mysterious past and special abilities naked inside a box. The crew dynamics and the way they operate have some parallels as well.
I was always a fan of FLCL for the soundtrack and ridiculous cultural references(Which I like much better in the dub - seriously who the hell references Richard Cheese?), but other than that just never really cared for comedy anime.
The Melancholy of Haruhi Suzumiya was enjoyable, and had an endearing quality to it despite having a lot of anime cliches in it.
My favorite is probably Evangelion, especially toward the end and the movies. And, it was the characters and character development that did it for me. You get to fully see most characters motivations, and it really delves into the human psyche while raising a lot of interesting philosophical questions. I can see why people wouldn't like it, though, but it really worked for me and I'm excited to see the retelling through the new movies.