I'm going to jump in here, and sort of raise a comment/question.
I've just been ripping several high quality (i.e., well recorded 16/44) CDs from Harmonia Mundi Italy, and found that on Exact Audio Copy, my compressed rips, which I think are still in WAV, are noticeably distorted on high tone vocals and complex passages. So I re-ripped now in uncompressed WAV format and there's absolutely no noticeable distortion. In fact the same songs sound fantastic through my system (HRT HD, Schiit Magni, Beyer Dt990 pro). The DAC is really important here, and I didn't notice such a difference before I upgraded to this particular DAC. (Of course I didn't notice a lot of things before I got this DAC, but that's for another section of this forum).
Anyone else notice this? I'm not a tech guy, but I can tell you what I'm hearing, and I'm 100% sure about it. It could be that simply the software used to compress these files introduces distortion, whereas an uncompressed rip doesn't get distorted. I understand that compression in this case requires software to compute where and how to compress the information.
It's enough to make me want to re-rip all my files that I ever ripped in compressed form. Darn it, the audio perfectionist OCD is kicking in now.....ahhh
Btw, this does not answer the question of FLAC vs WAC vs AIFF, but only compressed WAV versus uncompressed through the Exact Audio Copy software.
Also, note, I'm using HRT's USB ASIO output mode through Foobar2000, at the highest buffer and sample rates.