comparing the contents of entire CDs
 

Can K3B (or some other app) compare CDs to see if they are identical in content?

Save them as ISO's and compare the MD5sums?

Or cat or dd or whatever a mounted cd and pipe it to md5sum. For example: dd if=/dev/dvd | md5sum

I believe ISOs would be ok, as long as the CD only has one track. For instance, some CDs have a data track, and music tracks. I think an ISO would only capture the data track.

Capturing the disc with dd, as makuyl said, I think, would be your best option. dd should capture all tracks and data within.