Monkey's Audio for Windows

Monkey's Audio Homepage - home of the .ape

Monkey's Audio Frontend - recommended frontend for encoding/decoding purposes.
Current version is v3.99

Foobar - recommended player,natively supports ape, flac, shn etc...also encodes-decodes and more...
foobar2000_0.8.3_special recommended (no plug-ins necessary) - v3.99 compatible

Monkey's Audio for Mac

xACT - GUI frontend for monkey's audio (.ape), .flac, shorten (.shn), and shntool - v3.99 compatible
OS X 10.2 or higher recommended

Cocoa Monkey (frontend) - works on OS X and on older OS versions as well - v3.99 compatible

Pure Audio (ape player) - ape v3.97 compatible. (Not v3.99 compatible yet) Also plays flac and shn

Monkey's Audio for Linux

XMMS Plug-In - v3.99 compatible

Grip - Homepage of the Grip ripper/encoder, supports encoding to ape and others.