The game was released on 25 September 2007, about a month and a half before the episode 0107 aired in the US. Although there is nothing to specifically identify the game they're playing as Halo 3, though as they're playing you can hear the sound of recharging shields -- they clearly have been playing for a long time and were therefore playing Halo 2 before, it seems likely that they would be playing the latest version of the game since it had just come out.
It should be noted, that while some of the weapons, vehicles and terms they use are correct, Penny saying she "blew up Sheldon's head" in the game is impossible in Halo, unless she is using it as a metaphor. Also, when she sticks him with a Plasma grenade, she says "it's raining [Sheldon]", which is also not likely unless she means it's raining him in one piece.
Official website: http://www.halo3.com/