Check Foobar2000 to see if they have a plug-in for converting.
For ease of transferring or listening to on portables/CD's/PC's, in numerical order would start and end with MP3. For anything else, you're locking yourself into a specific portable (usually, although more widespread support is becoming available) or relegated to playing it on your PC only.
In order of file quality to file size:
FLAC
APE
OGG
MP3
OGG and MP3 are lossy, FLAC and APE are not. Buy a gimongous hard drive if you want to go lossless, otherwise, whatever you wish to settle for in quality is what you should go with, either OGG or MP3. EAC has OGG plug-ins, and I'm almost positive Foobar2000 either has OGG support natively, or has a plug-in to play 'em.
Obviously MP3 is the most ubiquitous format, but the other three are gaining as use of them is adopted. Going outside those 4 formats is a crapshoot at best, and even those 3 secondary formats have their own issues.
Check out
www.hydrogenaudio.org for a more complete breakdown and some further pointers. They'll also have a guide for setting up Foobar2000, which you'll need.