I'm really fond of the Fullmetal Alchemist score, particularly the "Brotherhood" theme. I enjoyed a few of the songs from the opening/ending credits, though not all. Last I'd checked, the US releases only cover a fraction of what the Japanese CDs do, which is a shame. (And I'm too cheap for imports...)
Naruto's "Konoha" theme is quite nice as well, as are a few of the opening and closing songs.
I enjoyed the .hack//Roots score. It's got some interesting variations on themes from classical music, plus plenty of original music. I happened upon the CD at GimmeAnime's booth I think at the last NDK (maybe it was Starfest?) and had to buy it. I'm glad I did.
Evangelion's got some good music, and I've got I think all but one or two of the various CDs they've released... which means I own about 12 copies of "Fly Me to the Moon."
Haibane Renmei's score is one of my favorite anime scores, and I picked up the soundtrack immediately after watching the show. Unfortunately, they domestic CD doesn't have the "Blue Flow" song from the end credits, likely for licensing reasons. (Naturally, if I bought the import instead, it'd be on there. *sigh*)
Millennium Actress had some fantastic music as well, though I've had trouble locating a soundtrack for it. I guess it wasn't popular enough in the US to get a release.
And, of course, one can't forget the music of Joe Hisaishi from Miyazaki's films. I particularly enjoyed the Princess Mononoke and Spirited Away scores.
As for the "best?" I couldn't say. I've not heard them all, and I don't think I could pick out the "best" even if I had. I've got a few that I enjoy more than the others (notably FMA, Haibane Renmei, and Spirited Away), but I'd have trouble even picking out a favorite. Cop-out? Sure. But there's no one soundtrack that sticks out in my mind as the "best."
