A lot of people on here use Exact Audio Copy with great success. My format of choice these days is FLAC since it works with the devices I need it to and it's lossless. I personally use Easy CD-DA Extractor, which I've found to be the most feature-rich and intuitive of the software I've tried, but it isn't free. I know at least one person uses dBpoweramp. I've used it to convert my audio files before, and it was worth the price of admission for that, though now Easy CD-DA Extractor supports multiple cores as well, so the gap may have been closed for speed.
Everyone has their own way of organizing their folders and files. I'm still figuring my method out. I tend to have artist folders with all of the tracks for that artist in that folder. The filenames contain artist, album, track #, and title. I find having all of this information in the filename helps from time to time on certain devices.
I'm not all that familiar with how Apple's system works, but it seems like a lot of people are happy with letting iTunes take care of everything. I'll let the iTunes experts give their advice.
