Remember the controversy that was aroused because of the fact that there was code in Oblivion that would allow PC Gamers and uber 1337 HexBawks gamers to have topless female characters?
The original Elder Scrolls game, Arena featured full frontal nudity for both male AND female player characters. There were also caves that had witch covens in them featuring hot, sexy sprites of completely nude witches in rather seductive poses.
Oh yeah, and those books about the Dunmer queen? The ones that have the sexytime censored due to draconian Morrowind governments? In Arena and Daggerfall, it reads like an erotic fanfiction.
Ultima 7 was heavily censored for its Super Nintendo release. The beginning scene where the one blacksmith is completely eviscerated is very toned down, and you aren't investigating murders, you're investigating disappearances.
When the original Crysis first came out, no computer could run it at the highest settings.
In a Duke Nukem 3D expansion pack, you can find a nearly dead green clad space marine surrounded by Satanic imagery that looks exactly like Doomguy. When Duke sees him, he states, "That's one Doomed Space Marine."
In Blood, a game made for the Build AKA Duke3D engine, you can find a hanging, mutilated corpse of Duke Nukem in a saloon. If you interact with it, Caleb says, "I got time to play with you" and, "Ooh, shake it baby."
Also, in Duke Nukem Forever, when you get the chaingun cannon, a soldier offers you power armor that looks exactly like the chestpiece and helmet of a certain Master Chief. Duke will refuse, saying, "Power armor is for pussies." I'm inclined to agree.
In Half Life: Opposing Force, a security guard will say, "Have you seen the new IG-88?" Apparently Black Mesa was developing assassin droids for the Empire.
If you type "ERVOS" which is SERVO backwards. at certain times in the PC version of Rebel Assault 2: The Hidden Empire, it activates Mystery Science Theater 3000 mode. Darth Vader, R2D2 and C3P0 will start riffing on the super cheesy FMV cutscenes in the game. Tom Servo is the red gumball machine robot from MST3K.