I would recommend WAV above FLAC, also if you're ripping your own CDs. Sure, FLACs are almost half the size, but storage is so cheap nowadays that I don't think that's an issue. Programs such as Mediamonkey support metadata for WAV files. If you want the files on a portable player then Mediamonkey can convert them on the fly for you.
It depends a bit on your setup; if you want the best quality playback, then there have been many credible reports that WAV sounds better. The reasons are not easy to understand as FLAC is supposedly lossless. However, this difference would only be noticeable on a high-end system and not on your typical hi-fi or computer music setup.