I recently started exploring the wonders of mk-table-checksum after spending too long dismissing the magic-like maatkit toolkit. What follows is not an exhaustive treatment of mk-table-checksum, but just an overview and some things I had to learn by trying the tool out.
The basic principle is based on the CHECKSUM TABLE table maintenance statement supported in the MySQL Server. The mk-table-checksum runs a CHECKSUM TABLE command on all (or some) tables. The results of that are stored in another table on the server.