For me, that physics engine is unparalleled. The way wind, gravity, electricity, water, and fire all interact so seamlessly and logically is something I've not seen in a big budget game. There's a lot to be said about a sandbox that gets it right--I can't think of another game (apart from maybe Half-Life) where you can go, "I wonder if this will work...?" based purely off your knowledge of real-world physics, and 99% of the time it will work.
Ok, right, I can't argue with that. That is truly something that makes it unique.