I haven't noticed any others, maybe I will have to watch them all again :-)
If you are a fan of first person shooters, particularly DooM, you should definitely watch the episode The Impossible Planet, as the whole feel was very DooM-like, and was definitely inspired by the game, which I'm sure is why they used the sample from the game. I think it was the best episode so far (including series 1).
Going to shut up now before I spoil it :-)
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moto