Do you have a specific need to use iTunes? If not, it may be best to avoid it, as it tends to be inflexible (I haven't used it much, but the one time I did, it infuriated me).
Here's some information on iTunes compatability with various formats:
http://www.itunesregistry.com/articles/flac/
Also check Ogg on Wikipedia...some interesting stuff there (although I have no experience with Ogg).
If you don't need iTunes, Foobar is a great way to go for playback on a PC. It's powerful, and open-source.
For ripping, EAC is excellent. It can be coupled with various add-ins that will convert audio files to other formats like FLAC. I don't know if it will convert to Apple Lossless.
To rip your CD once (and right), use EAC and rip to a lossless format (WAV, FLAC, etc.). Once you have the lossless file on your PC, you can find various programs to quickly convert to other formats, if needed. Some searching on the internet should yield a bunch of info on this.
As far as native goes, I'm not an expert, but I beleive it means that the audio data can be interpreted directly by the software or hardware, and doesn't need to be converted or translated in any way before playing.
So this should give you somes clues about what direction to go in on the software side; the hardware side is pretty tricky as well (assuming you've looking for high-end quality). Be patient, and spend lots of time searching on forums like these. Most of the info is there, just not all in one place.
