AgitarOne has had the ability to run hand-written JUnits since 4.2 but it was disabled in JUnit Factory until we were able to make them run in a safe sandbox.
If you have a lot of JUnit tests and you want a quick and easy way to run them and report on the results, request a Developer Dashboard and we'll run them for you on our server farm. They'll run much more quickly when they are distributed across 20 CPUs.
Developer Dashboards are great for open source projects. Just request a dashboard and send the resulting link to your team. Here's an example where one of the Cruise Control committers has requested a dashboard:
There are full instructions for Developer Dashboards at www.junitfactory.com/dashboards/.