elo--
As to your original question, you can keep WAV files organized in MC and tag them using MC's internal library. While MC does not generate a companion file for each WAV track as you hoped, you can export the MC fields to xml or spreadsheet and from there import them into many other programs, if you wish.
As for your concerns regarding audio quality, there is NO degradation when going from WAV to another lossless fromat, such as APE or FLAC. These formats are simply transcoding the original bits in a more efficient manner, just as WAV transcodes the original CDA image.
"Lossy" compression formats, such as AAC, WMA (lossy), OGG or the many variants of mp3, do not preserve the original bit-for-bit record. That being said, the sound quality can still be superb--just not bit-for-bit. Mp3 using the L.A.M.E. codec seems to be the expert's choice for lossy.
For a discussion of formats, try hydrogenaudio.org.