In my day job, I regularly have to convert/transcode/re-encode audio data from one format to another. Because I typically have to do this in batch jobs, I'm mostly dealing with command line tools (on Linux) like Lame, SoX (Sound eXchange), MPlayer and FFmpeg. Having a cheat sheet of how to invoke them with the desired options has proven to be very useful, so here is mine. Note that I only cover the operations I mostly need, like format conversion, sample rate conversion, conversion to mono and trimming/cropping. If you need more/other functionality, look in the man pages or ask your favorite search engine.
[Update] also see a follow up blog post about an execution time comparison between SoX, FFmpeg and MPlayer.