I guess I'd (and by that I mean, this is what I've done, but there's every chance someone has a better idea) write some kind of MongoTestHelper that can do a number of things during the various stages of your tests.
Before the test run, it checks that a test mongod instance is running and, if not, boots one up on your favourite test-mongo port. I find it's not actually that costly to just try and boot up a new mongod instance and let it fail as that port is already in use. However, this very different on windows, so you might want to check that the port is open or something.
Before each individual test, you can remove all the items from all the tested collections, if this is the kind of thing you need. In fact, I just drop all the DBs, as the lovely mongodb will recreate them for you:
for (String name : mongo.getDatabaseNames()) {
mongo.dropDatabase(name);
}
After the tests have run you could always shut it down if you've chosen to boot up on a random port, but that seems a bit silly. Life's too short.