Hi...
Hope you guys don't mind if I chime in with my first post here.
The choice of file method is largely one of your software and hardware choices as well as the intended use of the files - Archival or Playback.
IMO, archival files should be stored in FLAC because of that format's ability to retain metadata embedded in the file as opposed to WAV or AIFF. Because it is open source, moreover, it is more likely to be supported far into the future than are the corporate formats (AIFF and WAV) that will be subject to larger handshake concerns of the two software concerns (Apple and MS). I would keep that arcival copy as a reference and to use to copy into the format of choice for listening.
For listening, I would choose the format that coincides with the OS that you are using. In other words, if your playback is through OS-X (Apple), I would choose AIFF (or Apple Lossless if you really prfer it over AIFF, but there are other issues with regard to Apple Lossless, IMO). If the OS of choice is Windows, I would choose WAV. If one is using Linux, I would choose FLAC. The reasons are related to handshake issues between the file and the OS, and you are more likely to get the true copy of the digital file played back through the operating system that the file format was developed for.
The sonic differences, as to the extent they exist, will be at the far margins, but apparent to those whose hobby it is to hear those differences. I will say, however, that the assertion that there is a difference remains controversial, but one hears what they hear and it is my experience that one does not hear a difference between a FLAC file converted into a WAV file played through Windows and a FLAC file converted into a AIFF file played through OS-X or a FLAC file played through Linux OS - that latter combination is what I believe the high end audio arena needs to move in order to detach themselves from dependence on Apple and MS.
On the other hand, I do believe there are sonic differences when one listens to a AIFF, FLAC and a WAV file played through one OS - meaning all three compared on an Apple or Windows machine. I think that is what many people are hearing. My hypothesis, again, is that this is related to the software handshake issues that may produce some timing and/or jitter issues.
That begs the question as to whether it is simply better to rip directly into AIFF or WAV (I would not recomend Apple Lossless as the codec of that file system has and continues to evolve) in terms of sound quality. As a bit is a bit, there is no informational difference in a file converted from FLAC to WAV or AIFF or ripped directly from a CD into WAV or AIFF. In other words, the files will be identical making sonic differences both theoretically and practically impossible - at least if one is using a script like dBpoweramp to convert files. And, again, I would use FLAC for the archival copy because of its ability to embed metadata and its theoretical support lifetime.
That is my take, anyway.
