My favorite battle theme is the first Prime Cup theme from Stadium 2.
I also like GSC Kanto Gym Battle theme and the Crystal beast battle theme.
The Crystal beast theme was one of the awesome beta tracks from Ruby and Sapphire. o_o
It seems that I have a favoritism for gen II tracks but honestly I like most Pokemon themes except for B/W stuff
I'm gonna guess that the PMD games (Pokémon mystery dungeon) count?
If so, then the music in the Beach Cave.
For main games- Gold, Silver, and Crystal: Red/Lance Battle Theme.
Oh, and the end of the game music from Kingdom Hearts Two.
Guys, you should all hear PokeRemixStudio. He makes epic remixes of Pokemon themes!!!
A lot of video games have awesome music. Ace Attorney deserves a special mention though. But Mario, Zelda, Pokémon, Fire Emblem and a lot of RPG's and other games are certainly included too.
I can't choose a favorite(s), but here are the games I listen music from:
Earthbound/Mother (Very awesome!)
Super Smash Bros.
Legend of Zelda
Hg/SS Red battle music. Geez, that music is just EPIC!
also can't forget Final Fantasy and some other great RPG music
"Battle theme" from Final Fantasy X.
Seymore Guado's "Final Battle" from the same game.
^ Epicness on a stick. I also love Otherworld (the battle theme for Jecht, AKA Braska's Final Aeon).
Rpg music tiem
My favourite Chrono Trigger music:
Boss battle 1
Boss battle 2
The Black Omen
FFVIII boss music
Chocobo's own game's intro
Chocobo boss battle
Damn, I can't find more chocobo tales music.
Sands of destruction:
Whatever this is
How 'bout that. Next time I might do Ace Attorney music :3
Primal Dialga's theme from PMD2 is SPECTACULAR! but I also love spacial cliffs, team skulls theme, icicle forest, and murky forest. I like Colloseum's admin theme too though, not to mention XD001's theme from XD.