sox, which runs from the command line. It is one of the most un user-friendly pieces of software I've ever had to use, as all the programming effort went into making it work rather than making it look nice.
I've been having trouble with
soxtonight, in addition to all the troubles I've had already. But I remembered that I had problems with it once before, and wrote in livejournal about it. Aha! I thought, that's my answer. And indeed it was. Same problem as before, a bug in version 12.17.1, solvable by downloading version 12.17.3. Ah, 10 minutes of lj searching has saved me so much frustration :)