I've ripped most of my CDs to my PC's hard drive, using EAC and
storing as WAV (uncompressed) files. Sound quality, via the optical
out and into my Rotel 1066 processor into my Dynaudio speakers or Stax
phones is fabulous. However, experimenting with different players eg
Itunes, Winamp shows that the replay level on iTunes is substantially
lower than that of Winamp, and unless I'm mistaken, the quality
appears to be not so good. This leads me to think that the software is
doing something more than letting me just select tracks and is in some
way interfering with the actual signal. Am I right? If so, what's the
best replay software to use that bypasses any processing?

And while I have your attention, what's the best player to use to
"manage" a WAV library. Most seem to be built around MP3s. The only
one I've found that lets you "tag" WAV files (ie add album name,
artist, genre etc) is iTunes - but as stated I now have reservations
about the sound quality this produces.