Monkey's Audio (*.ape) is not a free-as-in-freedom format.
There are free implementations of Monkey's audio in Rockbox, ffmpeg and a JAVA one called JMAC (audacious's implementation is probably based on one of these three). The main issue with the format is high CPU usage while decoding, but this issue probably isn't significant for desktop usage (there are also other audio formats with high CPU usage such as Opus).
