I use Monkey's Audio (APE) mostly, for the following reasons:
1. I started off using it on high compression -- better than FLAC -- but with the size and prices of Hard drives nowadays, compression size is less of an issue, now I just use it on "normal" compression level, probably around the same compression as what the standard flac setting gives. I find it very fast, and when encoded as "normal" playback is very low CPU intensive.
2. It works so well with my favorite music software -- J River Media Center (the Monkey's Audio guy works for them too, so integration is painless). Media center does the tagging and replay gain well.
3. I find the Monkey's front-end software very easy, and the codec works so smoothly with lots of other freeware software, such as EAC, foobar, dbpoweramp and frontah.
4. I DON'T use an Apple Mac or Linux, nor would I bother with lossless on a portable player. As soon as I encoded into APE, I also transcoded everything to MP3 @ 256 to store on another drive -- which I can then use in an MP3 player or whatever.
5. I ruled out WMA from day one. I was just suspicious of Microsoft and this DRM (digital rights management) business. This was a gut decision, not a technical one.
In conclusion, choice of which lossless format (for me) depended alot less on compression ratio (they are all roughly the same) and more on how easy it is to use and integrate into my existing computer system and software. The advantage is that the day I want or need to change to another lossless format (flac, AAC, wav, wavepack etc) all I have to do is use a transcoding software and it'll do it while keeping all the tags and so on.
My advice to you:
1. Get a big hard drive and rip lossless, because ripping an tagging is a time-consuming pain in the rear and you'll only want to do it once.
2. Chose whichever lossless format works best with your system. But why use WMA when you also have APE, FLAC, Wavepack? Don't worry if you made the worng choice from day one, because in most case you can transcode between different lossless formats and you'll keep all the tags (I've done this from APE->Flac and vice versa).
3. Back-up EVERYTHING and store it in a safe place. This is essential.
4. If you need to transcode to MP3, MPC, WMA lossy, AAC or whatever, you can. But you'll always have your lossless master copies. And in a few years, hard drives won't be gigabytes, they'll be terrabytes and then petabytes.....
I have 967 CD's encoded as APEs. That takes up just under 250 GB.
hope that helps.