I like how the game rips of Metroid Prime 1-3 at the Metroid Database are put together, very complete, lots of bonus stuff and not remastered beyond recognition (sorry). My only gripe is the low-ish encoding quality, 128 kb/s at 32 kHz and I was wondering if better versions of these rips (preferably FLAC) are still around.

Metroid Database :: Metroid Prime Music (http://www.metroid-database.com/mp/music.php)
Metroid Database :: Metroid Prime 2: Echoes Music (http://www.metroid-database.com/mp2/music.php)
Metroid Database :: Metroid Prime 3: Corruption Music (http://www.metroid-database.com/mp3/music.php)

There's a trilogy release here ↓ (the flac links are listed in the replies and the MP3 is at the first page). I don't know if it has all of which you are looking for though.

http://forums.ffshrine.org/f72/metroid-prime-trilogy-remaster-project-flac-official-125632/6.html

Or use the search, I think there are quite a few files on this site.