JD and Elliot will always end up together...thats just the way TV works. Maybe this time it will actually last. JD pulled in a Friends reference so I'll go off that (though i can think of at least five or six other tv couples that would work). Ross and Rachel were on again off again for like 10 years, but in the end finally ended up together. It's the same way with JD and Elliot. They'll eventually end up together and happy and stay that way.