Alright, so I think I made some kind of discovery pertaining to the troublesome N64 games; This might not be news, but apparently different games' usfs play back at different sample rates. Taking a quick look at Winamp's sample rate indicator shows Mystical Ninja plays at 44Khz, Animal Forest at 32Khz, and Glover at 22Khz, etc. However, all .wavs that come out of the program are at 44Khz, despite the game fed into it.
First listen to this: http://dl.dropbox.com/u/16288082/Animal_Forest-6PM.mp3
-- It's 6 P.M. from Animal Forest played by samples that I extracted out of the game yesterday. I do not take credit for the transcription, I used a MIDI from here by Andrew Shand; If that's against the rules I apologize and will take it down, but I needed to test the sounds quickly somehow. Back to the matter at hand: I think it sounds good, nearly identical to the game, despite coming from one of the games that spit out lightning-fast, all-over-the-place .wavs.
The process I used was basically this: Any sounds that needed to be transposed (i.e. melodic sounds) I ripped right out of the quick .wavs without alteration, and exported at 22Khz as Blitz Lunar suggested. I don't think it had any detrimental effects to rip them as is. For the percussive sounds, I changed the playback rate down to 32Khz (i.e. the playback rate of the actual game), thus tuning the sounds down to the right pitch.
Of course you'll still have to wade through all the strange output of the troublesome games, but I think this experiment proves that despite that you can still rip sounds from them, to no (perceivable) ill effect.