Large hard disks are cheap, so the major shortcoming of wav -- lack of compression -- is not really a problem -- the advantage of wav is that it works everywhere.
Flac supports lossless compression, so files will be smaller (50% or so), and the sound quality should be identical to wav. the drawback is that flac is not supported everywhere -- macs, in particular, do not have good flac support out of the box. (someone can correct me if I'm wrong -- I'd love to see a quicktime codec plugin for the mac that fully supports flac, and is not abandoned). And of course, ipods don't support it either.
Personally, being a mac/ipod guy, I use Apple Lossless.
--Ian.