FLAC for Windows

FLAC Homepage - what is Flac?

FLAC Frontend - recommended frontend for encoding/decoding purposes.
here's an easy Flac Frontend Tutorial

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

FLAC for Mac

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

FLAC for Linux

XMMS Plug-In - plug-in for the XMMS player

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