Win:
Eac - audio ectractor, great safe mode, error correction algo and a LameFrontend as well
http://www.exactaudiocopy.de/
*nix:
http://www.xiph.org/paranoia/
Lame mp3 encoder for most platforms. The "--alt-preset standard" switch is a great hq Vbr MP3 setting.
http://mitiok.cjb.net/
http://www.mp3-tech.org/
General info on audio compression:
http://hydrogenaudio.org/
Any more info needed gimme a shout.. (or pm