Not that I'll ever be able to drive either one (though I have seen both) I great prefer the F50, for no other reason than the engine and the quality. They are both great....but the small displacement, high revving V12 is simply wonderful.
It's difficult to understand how impossibly exotic the F40 looks in person, especially around more humble cars. It looks like it came straight from LeMans. The F50 isn't quite as good looking, but I still love it's very integrated and cohesive body design, something that has been lost in recent years with the trend of sticking on splitters, spoilers, air dams, diffusers, winglets, and the general idea of 'subtractive' body design. The F50 looks simply solid, and I love it.