In the case of flac versus .wav, I would expect if everything is working well, and the resolution of the files are the same, there should be no inherent difference in sound quality resulting from format alone....
Ok, I've done this experiment with at least 20 audiophiles and PCs ranging from Pentium 4 to Core i5 (laptops, desktops, Wi-Fi, USB, PCI, Squeeze Server, DB Power amp, Foobar, J. River Media Center, etc.), and they did not know what's playing (blind A-B test). Somehow they all preferred WAV. All had a hard time choosing between Monkey's and Apple lossless, and all disliked FLAC because, in their opinion, it sounds thin and with unnatural/mechanical top-end.
Interestingly enough, I've recently talked to someone who has a famous audiophile recording studio. He also dislikes FLAC because of the same above mentioned reasons.
If someone around here has the same experience and has a remedy, Id be more than happy to experiment and report back. For now if lossless is a must, I am sticking with Monkeys Audio, but that is only for not so good recorded material.
Best,
Alex Peychev