FLAC can be used to codify a WAV file keeping the integrity of the original signal. The codec comes with a little tool which facilitates the compression. It´s not necessary to use the command-line.
For now, not all the multimedia players, audio convertors or sound editors support FLAC; that´s why on the programs web you can find plugins and instructions to be able to use the codec in applications like Windows Media Player or dbPowerAMP Music Converter.
FLAC also includes a tag system which allows you to save information about the audio file.