Here's a little, simple-as-possible Perl script I put together for finding tracks missing from album folders. It moves through a music collection, queries MusicBrainz (using AudioFile::Identify::MusicBrainz) and, if the number of tracks doesn't match, produces a list of the missing tracks for each album. It also incidentally downloads the cover art from Amazon for each album and saves it in the album folder.
I wrote this for my own collection, so it only works as provided if your MP3s have filenames ending with the track title and are within album folders, within artist folders, within one base folder, which is how iTunes organises files.
Download AIBrainz for OS X/UNIX.
(Windows version to follow soon, it has to be slightly different).