If they're already in the form of video files, I think ffmpegx (free) also does this.
It would be great if there were an app that in a really simple way (like iSquint level of simplicity) took a DVD of a concert / musical / etc (in which the tracks correspond more or less to the tracks on the soundtrack) and just let you click a button, rip all the chapters into separate AAC files, populate the ID3, and put them in iTunes. But I don't know of anything that simple. 🙁
Although, in your case, probably what ffmpegx, Audio Hijack, etc, do would be fine.