The ones I want are the ones that (I think) are least likely to occur:
Chaos Marines vs. Inquisiton
Adeptus Sororitas vs. Grey Knights
Imperial Guard vs. Chaos Cultists
Preheresy: Iron Hands vs. Emperor's Children
Preheresy: Mechanicus vs. Iron Warriors
On a side note, has there ever been a starter box that didn't have marines of some kind?