In July 2013, I would have said it's a tie between two sets:
7037 Tower Raid and 6242 Soldier's Fort.
But since then, I've had two close runners-up:
70816 Benny's Spaceship, Spaceship, SPACESHIP!!! and 70620 Ninjago City.
I'll have to decide again if there's any that could dethrone 6242, which is my favorite LEGO set of all time. Lots of good play features, plenty of minifigures, modular structures for different sceneries, comprehensive yet sturdy build, and worth the $50 USD MSRP.