[TippeX]

some protections slow things down depending on whats done...
code converted to vm obviously runs slower because it has to be interpreted runtime
most of the time the unprotected exe will run faster, but thats a given really because there is no protection layer..

for example i had a game world in conflict, where i had the protected exe and the cracked one, the cracked one ran about 5-10 frames per second LESS than the protected exe.. and chances are high that the unprotected exe was faster than the protected one...

so really, for some cracks the method used to do the crack can result in the program running slower than the protected exe...

and the developers can also (judging from the sdk's i read) mark various portions of code to not be protected, vm'ed and so on, so they do have some control...