Daedalus_audio - Apple lossless is indeed lossless. You can convert a WAV file to Apple lossless and then back to WAV and the original and converted WAV files are bit for bit identical. You can rip a file to Apple lossless and convert it to WAV and it is bit for bit identical to a WAV file ripped directly to WAV. Are you sure you have checked the box to do error correction when ripping with iTunes? If you are hearing major differences between Apple lossless and WAV then it is probably a playback issue or some other software issue, not a issue of Apple lossless being "lossy". There are lots of very detailed discussions on this topic and some people think there are subtle differences between various formats. There may be some minor errors is some of the software, but the actual data bits are the same. Since Apple does not provide details on its file format, it is very hard to analyze the various meta data in the file.
Mmike84 - I would suggest you look at dbPoweramp. It has a batch converter and I believe it can convert AIFF (or FLAC) to WMA, although I have not tried it. Note that WAV and FLAC files do not have embedded tags.
