Flippant comment, but there’s some serious truth in this. Data you haven’t backed up is data you don’t want. Time Machine makes backing up trivial to the extent that it’s a zero button solution. I plug in my external hard drive, it recognises it as a Time Machine backup and automatically syncs any changes since the previous backup.
Time Machine makes backing up trivial to the extent that you have a sufficiently large HFS volume sitting around, and don't need to back up MySQL databases. And if you're unlucky, it can also automate the process of losing all your data:
What's the MySQL reference to? I haven't heard of a MySQL-specific issue with Time Machine.
If I understand correctly, Time Machine takes a binary snapshot (similar to rsync). With MySQL (and InnoDB specifically) the stuff on disk is not guaranteed to be in a consistent state while the server is running. The safest way to back up mysql is mysqldump.
For me, at least, every time I reinstalled Leopard and restored with Time Machine MySQL's data would be gone.