All right, time for some music suggestions! As of now, I'm covering Zelda and Metroid, but I'll probably kick out a few others in a little while.
We have a nice set-up here thus far. However, may I suggest:
Hyrule Castle Interior (Twilight Princess) - This mix gives me the chills. It's an excellent blend of LttP's castle theme and Ganon's theme from OoT.
Hyrule Castle (Wind Waker) - This slow, sad theme would work as a nice change of pace...perhaps Slow Brawls would benefit most from it?
Hyrule Castle Sneaking Theme (Ocarina of Time) - Kind of goofy music, but I think it could work here.
I imagine this stage having some of the more unique Zelda tunes in the series.
Windmill Hut (Ocarina of Time) - A kooky song that I think works with the background. It'll get faster as the Moon gets closer to crashing, but will reset once the Giants lift it back in the sky.
Spirit Temple (Ocarina of Time) - Probably my favorite dungeon music from OoT, this would work quite well I think with Termina.
Sailing Theme (Wind Waker) - Since this does take place over the ocean, why not use the theme from Wind Waker as well?
Dungeon 9 (originally from Legend of Zelda, but use the Four Swords Adventures mix) - Surely a stage featuring some gloomy imagery could have a gloomy song to accompany it. The remix in Four Swords Adventures was very well done, so I would lean towards using that over the original.
The Temple lends itself to many dungeon themes, including:
Dungeon (Legend of Zelda, unedited) - This iconic tune would fit like a glove, methinks.
Forest Temple (Ocarina of Time) - This theme has some cool instrumentations, which could lend itself to this stage quite well.
Temple of TIme (Twilight Princess) - I liked the theme for this area a lot. It had some echoes of the original OoT theme, but twisted it around into a different tune. Quite nice.
Overworld (Link's Awakening, unedited) - I've always thought this was one of the better overworld themes, so I'd like to unitize it here...minus the techno feel of Brawl's mix.
Metroid has some awesome themes...I must admit to being a tad disapointed at the lack of choices thus far.
Creteria (Metroid Zero Mission) - A catchy mix of the original Metroid theme.
Planet Tallon (Metroid Prime, unedited) - I love this music. It captures the essence of Metroid, and I think it could work very well here.
Tourain (Super Metroid) - Creepy music. Tourain is one of the creepiest levels in gaming history in my eyes, and having that music ought to make battling tense.
I have a ton of ideas:
Brinstar Overgrown(Super Metroid, unedited) - I love this music, and I think it'll work very well here.
Mother Brain Battle (Super Metroid) - Since Mother Brain is plopped in the background, might as well figure in this tune. I imagine a nice techno remix...
Item Room (Super Metroid) - Since a Chozo Statue is wandering about, I thought this slow, calm music could work out quite well here.
SR-338 (Metroid II: Return of Samus) - I like this theme, and hearing it remixed would be awesome indeed.
I imagine a lot of slower themes working here.
Maridia Sands (Super Metroid) - I imagine this working out fairly well here. It's a very mellow song, but the stage, outside of Kraid's rage, is fairly calm itself.
Magmoor Caverns (Metroid Prime) - This nice drum beat this features could work out well for this stage.
Title (Metroid Prime 2 Echoes) - I really liked this intro music. Very catchy.
Space Pirates (Metroid Prime) - Another excellent battle theme, one that I think could fit in with this stage.
That's all for now, but I'll have more soon, I'm sure.