Depends on what your priorities are. And your ears.
For instance, if you have unlimited space, APE - significant file compression, lossless.
MP3 is the most widely supported format, and it gives you very significant compression if space is a consideration, but a lot of people believe that it is so-so audio, at least until you get to 192-224 kbps, and at that point, you're losing some of the compression advantage. If you're going to use mp3, a lot of the users here recommend VBR.
WMA gives the most substantial compression (I think), and has some supporters, but a number of others feel the audio quality is inferior.
Ogg Vorbis (IMO) gives very high quality. It's slow in the encoding process, and is not as yet widely supported in Hand-helds and other programs. You can always rip as .wav if you've got the room, then do a batch convert in MJ overnight.
You really have to listen to figure out what you think the best quality audio is - say, rip/encode the same track from a CD in MP3 224 VBR, WMA at 96 or 128, O/V, APE, then play them consecutively at the same settings. Once you nail that preference down, compare file size, speed in encoding, think through how and where you'll be accessing the files, go from there.
No off-the-shelf answer. De gustibus non disputandum est.
HTH
Listening to Dave Douglas - 'A Thousand Evenings' on Rhapsody (home computer is defragging ATM, so can't access MJ)