MySQL is released under the GPL, which means that if you bundle it with a non GPL application (e.g. for a commercial project) it is not free. You must purchase a commercial license then.
This is not limited to "bundling" the MySQL binaries (e.g. embedded usage), but as far as I know this already qualifies if you just add e.g. the connectors. But I'm not 100% on that. The exception in the license for e.g. the JDBC driver is only understable for a lawyer.
I always thought that. An ISV that I know of has an application that can use MySQL as a database, or SQL Server. They claim that they have been getting billed from MySQL and for that reason are pushing the free version of SQL Server.