Just thought I'd mention this one here, since I have yet to see anyone else on the board mention it (forgive me if someone else has...).
ShnTool was originally designed as a utility for manipulating Shorten and WAV audio, but it's progressed far beyond those humble roots; the current "1.2.0-rc1" release also supports AIFF, FLAC and APE files, and offers the ability to directly convert between any of those lossless formats. (Sidenote: A while back I wrote the author of WavPack asking whether he would add WV support to ShnTool and received a positive response, so support for this format may also be forthcoming.)
No, I'm not connected with the ShnTool program in any way - but it's one of the most useful on my entire system. Anyone who is interested can download the binaries and "helper programs" (to allow ShnTool to parse the formats mentioned) from this site: http://shnutils.etree.org/shntool/
- M.