Flying stage, flying stage. Hrrm.
-"Asteroid Run" from Cybernator/Assault Suits Valken is pretty funky.
-"The Flatter Vs. The Geshell Shaft!" is the excellent latin (?) song from the long air battle in Rockman Legends, if I remember correctly. Probably the best VGM song of it's type aside from SOTN's "Wandering Spirits"
-Both Zero 2 and Zero 3 have neat "flying" stages. Zero 2's "Power Bom" is easily the better BGM (pulling off some pretty amazing rock on the GBA). Zero 4's "Celestial Gardens" probably also fits the bill, with it's nice MMX vibe, although it's one of the less impressive songs in the game.
-The Area 8 BGMs from Ganbare Goemon 2 is really sweet. Short, but great final stage themes.
-The Band Land levels in Rayman seemed to take place in the sky, and the first BGM for them was simply beautiful.
-MIDAIR GIANT PLAYGROUND BATTLE! Tsuyoshi Sekito is a fucking
master, and Brave Fencer Musashi is proof of that.
-Some other Squaresoft flying dungeon themes of note: The Black Dream (Chrono Trigger), Sentinel (FM: Gun Hazard), The Excitement of Both of Us (Legend of Mana), Leave Time for Love (Secret of Mana). Shit, Square pretty much has this market cornered.
-Stage 3 theme from Gunstar Heroes (and by extension, Gunstar Super Heroes).
Oh, and Ganbare Goemon 4 has an absolute awesome stage where you're dropped out of an airship while standing on top of a car (?), and you have to fight enemies on the way down. It's a short level, and the music is also short, but both are awesome. Then again, Ganbare Goemon 4 is such a fucking great platformer that it should be required playing. Quite possibly the best music in any SNES game, too.
Of course, none of this is counting music from shmups. We'd be here all day. Ditto goes for airship themes.
But if we are going to allow non-shmups with shooter stages, then this thread is fucking hands down won by the
level two theme from Astro Boy GBA. It starts out strange, but it's an excellent song, and fits the game beautifully.