The image files I burnt from were bin/cue or ccd/img/sub compressed via ECM. (For those who don't know about it, read up on it here: http://www.neillcorlett.com/ecm/) Obviously, I uncompressed them to burn them.
Another thing which bothers me is the fact that, with some games, skipping video/missing audio seems to persist even on emulators. For example, my image of Psychic Force: Puzzle Taisen won't play music at all (even though audio tracks are present and will play on the CD player menu) and Suikoden II has a jittery opening video.