I've seen Gamers 2 several times now, but I've never been sure which RPG they're supposed to be playing. I believe it's supposed to be DND 3.5, but I am not sure on that. So, are they playing 3.5? How can you tell? If not, what are they playing?
You are correct in your assumption that they are playing DnD 3.5.
More specifically, they are playing the module called The Mask of Death, which is a real game.
From the Mask of Death link:
This module is a special limited edition produced exclusively for Gen Con Indy 2005. It presents chapter one of an adventure that chronicles the hilarious escapades of the hit film The Gamers: Dorkness Rising.
More info. can be found on the wiki page.