I'd actually stick to FLAC personally.
I ripped my CDs once to WMA because I had a Zune and it seemed like a good idea. I then re-ripped everything later to MP3. While I don't hate MP3, I prefer lossless, so now I'm going to to re-rip everything as FLAC in hopes that I won't be tied to a specific vendor or system.
And if you use J River Media Center, as others have stated, you'll enjoy the best of both worlds.