Here's some great audio oriented tools:
LAME mp3 codec
v3.96 is the latest stable build, however, 3.90.3 is still the most tested.
Musepack
Musepack (mpc) is a compression format for music similiar to mp3 but offers generally higher quality at a lower bitrate. It's main advantage is that it works solely in the time domain.
Foobar2000 : IMHO, the best audio player, tagger, diskwriter, converter, etc available.
MP3Gain : Reduce clipping in those mp3's, or use it to make your mp3's all have the same volume.
ReplayGain : The same concept for other file types.
Exact Audio Copy : EAC is the only ripper that rips in a secure mode that verifies that your rips are exactly what is on the cd. Helps to rip those scratched cd's without audible clicks and pops. Also supports most codecs with a .dll and any codec with a CLI.
FLAC : FLAC is essentially ZIP for .wav files. A lossless encoder.
Monkey's Audio : Similiar to FLAC, but *perhaps* not as robust. Generally slightly faster with slightly better compression.