Assume you have a whole mess of WAV files that you want to convert. First let's turn them into MP3s.

lame --preset insane *wav

This basically creates the mp3 at 320, which is, uh, insane, but it's the highest quality level. If its not 320, I don't want it. You may choose 192 or above; unless it's speech, I would NEVER use anything less than 192.

Now let's convert your WAVs to FLAC files.

shntool conv -o flac *.wav

If you're using a Debian-based system, you'll probably need to do this first:

sudo apt-get install shntool

Is that not easy or what?

(Check out all of our posts on conversions, WAV, MP3, & FLAC.)