For me, most of the best music is actually found in the spinoffs. My favourite is the GBC Pokemon Trading Card Game's Club Leader theme. It really makes you think of an epic battle... not a couple of people playing a card game. Heh.
Pokemon Pinball on GBC had some pretty good tunes; the blue field catch 'em music is about the only one I can find right now, but there are some good ones.
Pokemon Puzzle Challenge was fairly vanilla for music, though I do dig the Goldenrod City remix.
And to show you that I'm not just slurping the GBC, I also thought it was great the way they used '2 B A Master' tracks in Puzzle League... Favourite is Erika, but I dig Surge too. Think that one came from the anime.