Apple Lossless, AIFF or WAV for itunes?

Since you said "for iTunes" you won't use FLAC unless you use
a third party player software that works in tandem with iTunes since iTunes
does not directly support FLAC. my choice would be AIFF or ALAC
because of the metadata support and I personally do not hear a difference
between any of them.

@Macdude

If you are comparing a download (WAV) with a CD rip (FLAC) you may well be comparing much more than the difference in audio codecs. They might be entirely different masterings or mixes. Unless you could be certain they are from identical sources you could not be sure.

You could rip your CD to WAV and then to FLAC and that would ascertain a valid comparison.