In the scripts of Dead Island, Purna's "Gender Wars" Skill is sometimes referred to as "FeministWhore". This caused some controversy when discovered, and Techland issued an apology, saying that those responsible would be terminated. You can find the apology here: http://kotaku.com/5838387/dead-island-ma...hore-skill
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In Quest for Glory, if you have a high enough skill, you can 'pick' your nose. Characters react to it if you do it in front of them:
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In Sonic and Sega All Stars Racing, a developer accidentally used a picture of Sonia, from Sonic Underground, on one of the playing cards in the Casino level. It was lifted from a Deviantart user, and Sega was forced to apologize.
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In the mod Cry of Fear, if you run up a curved slope and open the door, you will find a secret room with a golden statue. This is a reference to the Youtube Let's Player Pewdiepie, who is friends with the creators of Cry of Fear.
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There is a special AK-47u reload animation that plays in the Mission "Turbulence" when the plane is going down and you are floating in Zero-G. It cannot be preformed anywhere else.
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(I apologize if someone has already submitted most of these.)