I'm in process of ripping my 600~800 CDs to flac now having bought a Squeezebox and recently added a Transporter.
I use EAC. It's actually not hard to set up. The myriad number of things you can do are what make it a little overwhelming at first. The best thing to do is go to the hydrogenaudio.com forums or just search in google for flac and find the hydrogenaudio link. They have a page that tells you exactly how to set it up using flac as the compressor. It's worth it to spend a little time doing this. They'll tell you the command line and another place how to set up the tags. Very nice. Or if you want I could just send you my EAC profile which'll have all that stuff.
Compilation discs, soundtracks, musicals and classical discs can import with some unexpected results for file names, artist/composer names and folder structures.
Yes, definitely a good point. For those cases above, I uncheck various artists and put in whatever I want to reference it by. For example a classical CD of Mozart will be tagged by the pianist (under artist in Transporter). Just change the Artist to Mozart (and uncheck various). The Pianist's name will still be in the file name. But it won't cause your Transporter display to show all these other names other than what you know it by. If you have a compilation or soundtrack and don't do this you'll have all number of things to sift through when trying to find what you want.
regards, David