Among the dungeon tracks, two particularly awesome ones are The Withered Forest for the 4th Stratum, and the 5th Stratum Music. (The name is a spoiler.)
Even the event music is awesome. Ladies and gentlemen, Blue and White.
The battle theme of the 6th stratum Ecstasy ,considering that it's the battle music that only plays in the Bonus Dungeon of an already Nintendo Hard game, the only thing matching it's awesomeness is the difficulty.
Rising Again sums up the battle it is in perfectly.
In general, thanks to the live orchestration, it's a little tempting to link the whole thing. Yuzo Koshiro really blew it out of the park this time.
For starters, though, Battlefield - Storm is the normal fight music for the early dungeons. And when that's just the normal fight music...
All of the music in the Scarlet Pillars land is great; The Red Stone Forest lets you know you aren't dinking around in kiddie land anymore, Led Astray In The Lost Woods is suitably grim-sounding for places like the poison-filled first cave where you must find the fuel to make the skyship go higher, and The Misty Ravine balances the mystery, wonder and danger of the second dungeon perfectly.
On that note, of course, Windy Plains is also fantastic as music for the first overworld area; you've got an AIRSHIP! And you're going on ADVENTURES! And then you get punched by a kangaroo.
So you liked End of the Raging Waves? You did? Well, how about End of the Raging Winds? Warning: your ears are probably not ready for this.
Taken from the 'Live Music by Piano and Strings: Sekaiju no Meikyu I & II Super Arrange Version' album, we have excellent remixes of Cherry Tree Bridge and Blue and White.