Hmm, a couple of years ago I made a "Top 25 Pokemon music" list, though it contained some non-battle themes as well, and only counted music from the main-series games (i.e. no Colosseum, Mystery Dungeon, etc.) But the battle themes from that list, as well as a few more I like, are: (in no particular order)
- Final rival battle theme (R/B/Y), as well as its FR/LG remix. I especially like the intro of the latter one.
- The original gym leader battle theme of Red and Blue. It's been remixed several times, but the original is the best IMO.
- The Kanto Wild Pokemon battle theme in HG/SS. Techno-ish music remixes FTW! Same goes for the Johto gym leader battle theme.
- The Champion battle music from HG/SS. MUCH better than the original IMO. The opening is especially epic.
- Frontier Brain battle (HG/SS). So catchy!
- Kyogre/Groudon battle music from R/S/E. It just works so well against those drums in the background.
- Battle with Suicune in HG/SS. I like how the three legendary dogs have different remixes of the original theme, but I like Suicune's the best.
- Battle with the Lake trio in D/P/Pt. I really like the melody of this one, especially with the bass line in the background.
- Cynthia's original Champion battle theme from D/P. None of the later remixes just felt as epically awesome as that one... though the B/W remix is kind of nice too.
- The music that plays when a gym leader's down to their last Pokemon in B/W. What an awesome addition that was.
- Battle with the Team Plasma grunts in B/W. I actually like this better than the B2/W2 remix, because the beat brings out the melody more.
- Ghetsis' battle theme in B/W. Chanting Ghetsis' name in the background = ultimate bad*****ery, like One Winged Angel-level bad*****ery.
Of course, though, the only Pokemon tunes I actually have as ringtones are non-battle ones-- they're the Driftveil City music (my favourite city theme of all) and the Radio Tower takeover music from HG/SS.