Cowboy Bebop, no contest. Yoko Kanno killed with this one and has been reigning supreme ever since. lol
Samurai Champloo has a fantastic hip-hop soundtrack, Baccano! has some nice jazz going (though not as nice as Bebop), Wolf's Rain and Ghost in the Shell are also Yoko Kanno works, and I'll thrown in FLCL, too.
Mushishi's my personal favorite right now and it's fantastic. It's essentially a bunch of eerie-sounding easy listening music, but it's really beautiful stuff, man.