I had a play with MongoDB JDBC but now FME has that as a supported format.
I have not used any JDBC formats in FME Desktop.
But I have used JDBC connections in the FME Server environment (connecting to SQL Server):
DB_DRIVER=com.microsoft.sqlserver.jdbc.SQLServerDriver
Had a customer using JDBC to connect to Oracle but we then install a client and saw a big improvement in performance!
I have used jdbc RW from SAP HANA (I think before native support on the W (for the Win ;)
A weird one I have read filemakerPro tables > SQL Server using JDBC connection string. jdbc:filemaker://$(server)/$(table) using the jdbc driver which comes with FileMaker (fmjdbc.jar) installer materials
And Neo4j as per Raven's blog, but i was told recently i need to speak to @ulfme about Stardog (anyone up for a Graph db sidebar in Vancouver?)