To monitor mysql, you need to activate the mysql pid file creation. In /etc/mysql/my.cnf, in the [mysqld] section add

pid-file = /var/run/mysqld/mysqld.pid

To run munin with apache and mysql monitoring, you need to install two perl modules.

aptitude install libwww-perl libcache-cache-perl

Or else munin-node-configure --suggest will report LWP::UserAgent not found and Missing dependency Cache::Cache