Are you trying to do this for a PC based archive? Or an iPod or something? Do you have a preference for interface? iTunes?
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Here's a little primer...
WAV and AIFF are "wrappers" for PCM data, the first generally used in PC environments and the latter in Mac. This is, in effect, a "raw" CD data file. Since these are just wrappers, they don't have a lot of added stuff, like tags, and they are unprocessed--not compressed at all.
There are two kinds of compression. Lossy and lossless. Lossless is just that--a reversible process whereby the original can be recreated bit-for-bit. Lossy involves more severe compression and the elimination of data that coders believe is not as audible.
FLAC and Apple Lossless (ALAC) are both compressed, but lossless, and have the benefit of supporting tags. WMA is the new standard for Windows media, supporting DRM and stuff. Seeing a .wmv extension on a file is like seeing a .m4a extension--.m4a may be an ALAC, or it may be a severely compressed AAC (lossy compression). Seeing .wma may be lossless or it may be mp3-like compression.
In other words, not all .m4a or .wmv files are lossless, so you really need to confirm what you are ending up with. But, at the end of the day, lossless should be, in fact, lossless. Just a smaller file size.
As far as sound quality goes, might look up some posts by Audioengr, I think he mods Transits to improve the clock, and I gather Transits take modding well. I personally dislike toslink, so you might get him to install a coax output instead too. ;)
Personally, I use a Waveterminal U24 USB audio device, but I gather from another thread that they discontinued them. :(
As far as the other parts, many will recommend foobar as a great player, and indeed it is. Unfortunately, foobar doesn't like Apple Lossless and I find the interface a bit non-intuitive. Apple does great UIs, so I'm sticking with iTunes.