Originally Posted by Galley
Size differences aside, Apple Lossless supports tagging; WAV does not.
This is a deal breaker for me and the reason I went with Apple Lossless for ripping my CD's. FLAC is pretty good, but seeing as how iTunes is how I listen, transfer, organize and manage my library in general, I figured I'm killing two birds with one stone by using Apple Lossless. It's nice to be able to re-encode your music to a lossy format and have your tags filled out for you automatically in the process.