A few months ago I decided it would be good to re-rip my CD collection, retaining a lossless digital copy, and set about planning the project. I then realised I hadn't the time to take the project on for the time being and parked it, but not before figuring a few bits and pieces out.
Starting at the beginning, with ripping the CDs. The most widely used CD ripping software on Linux systems is still cdparanoia, which is pretty good, but it's still possible to get bad CD rips, and I've had several in a very small sample size. On Windows systems, the recommended ripper is Exact Audio Copy, or EAC for short. EAC calculates checksums of ripped CDs or tracks and compares them against an online database of rips called AccurateRip. It also calibrates your CD drive against the same database and uses the calculated offset during the rip.
I wasn't aware of any AccurateRip-supporting rippers until recently when Mark Brown introduced me to morituri. I've done some tentative experiments and it appears to be produce identical rips to EAC for some sample CDs (with different CD reading hardware too).
Fundamentally, AccurateRip is a proprietary database, and so I think the longer term goal in the F/OSS community should be to create an alternative, open database of rip checksums and drive offsets. The audio community has already been burned by the CDDB database going proprietary, but at least we now have the—far superior—MusicBrainz.