If you know anything about shell scripting you should be able to "whip up" a script to use ffmpeg which is a free converter from Unix/Linux land.
dBpoweramp and XLD are perhaps the most popular. XLD is free. Convert your files to aiff or alac. Keep in mind if you choose wav it doesn't support metadata like other formats.
The age-old wav vs flac debate has been raging for years now with strong proponents on both sides. Listen for yourself if you care to. While I respect Steve's viewpoint I don't agree with him and I assume he won't be the one listening to your system.