Monkey's Audio is a lossless audio compression algorithm. The codec uses the ".APE" file extension, so if you come across them, you'll know what to do.
I've found that xAct is the best GUI app for these files. But if you're looking for command-line tools, your best bet is at Sourceforge.
I had been using version 3.97 successfully until I received an "Error: 1002" while attempting to decompress an ape file. Googling turned up the following on the Monkey's Audio forum: