I\'ve inherited a load of Junit test, but these tests (apart from most not working) are a mixture of actual unit test and integration tests (requiring external systems, db e
I would move up to Junit4 just for having it :)
You could separate them into different test suites. I don't know how they are organised in Junit3 but it should be easy in Junit4 just to build up test suites and put all the real unit tests in one of them and then use a second suite for the integration tests.
Now define a run configuration for both suites in eclipse and you can easily run a single suite. These suites also could be launched from an automated process allowing you to run the unit tests every time the source changes and maybe the integration tests (if they are really large) only once a day or once an hour.