I had faced a similar issue wherein the method DataSource.getConection() would simply hang forever without any response. My development environment had Tomcat 5.0, Connector/J 5.1.6 and MySQL 4.0.
The problem was with the MySQL connector. The Connector/J version that I used was incompatible with the version of MySQL server. I then used Connector/J 5.0.8 which resolved the problem.
which version of connector/J do you use?
You can find more info here MySQL Connector/J documentation