RuggedCircuits:
You can run a ULP that will place tRestrict circles around through-hole pads, which will prevent routing away from the pads on the top layer. Then there will be no need to solder these pads on the top side (where they are obstructed by parts).
Beautiful and clean solution. Learning something new everyday, which when it comes to Eagle, it means I now know 0.2% instead of the 0.1% I knew yesterday! 
I drew a (bRestrict) rectangle covering pins AREF down to D21 and so on (Mega) and it did it in 2 seconds what I had spent the whole day yesterday doing by hand. I had the top layer cost high and it created just a few vias, which I can easily just solder a piece of wire connecting both sides.
Thanks a zillion!