This would also fit under Databases, but since the trouble is (most likely) Debian specific, I'm putting it here.
If you still have tables in ISAM format, you may want to convert them now. The current testing distribution contains a conflict with libreadline4 which forces an upgrade from MySQL 4.1 -> MySQL 5.0 as soon as any package that depends on libreadline5 is installed/updated.
MySQL 5 then refuses to install when it detects ISAM tables. The only way out is to reinstall libreadline4 (and have APT uninstall all packages that depend on libreadline5) + MySQL 4.1. Then do the conversion, reinstall all the dumped packages again and switch to MySQL 5.0.
(The underlying conflict is caused by readline-common which conflicts with libreadline4/stable. It references libreadline4/unstable, but that one only exists for kfreebsd and the source package is AWOL).