Reference 1: Quite early in the game 'Prototype' you get to know that the name of the main character is Alex J. Mercer. If you have seen the first Robocop movie you might remember that the main characters name is Alex J. Murphy.
Reference 2: In prototype when you have the full-body armour activated you almost look like a black version of Robocop.
Perhaps the fact that Alex from prototype is amnesic just like Robocop isn't just a coincidence... It might be a third reference.
Also, another thing I just realized: They both died once. emcc - Sep 26 2010 3:04AM
I just remembered... Another thing they have in common is that both of them have thermal vision. emcc - Sep 18 2010 9:40AM