Is there handy code coverage tool to be used with JUnit?
Cobetura http://cobertura.sourceforge.net/
There are many and google is your friend.
NoUnit
Coverlipse (I would recommend this, but its an eclipse plugin)
Codecover
I would imagine most code coverage tools can be used pretty easily with JUnit. Previously I've used EMMA, which is good. If you're an Eclipse user, there's an Eclipse plugin called EclEmma to integrate things.
Here are my preferences in that order:
And here is a bunch of open source tools and with comparison.
Hope that helps.