There's a full book you can read in Deus Ex. It's called The Man Who Was Thursday by G.K. Chesterton and shares some plot similarities with the game. The chapters were spread throughout the game in datacubes.
If you cheated while playing the Sega 32x version of Doom, after the game ends you're taken to a fake DOS prompt. You can't quit out of it, and the only way to escape the screen is to reset the console. If you didn't cheat, you get an extra cutscene.
The voice of Shodan, the insane AI in the System Shock series, was performed by the wife of the audio director at Looking Glass.
In World Of Warcraft there's a dungeon called Uldaman where you can find and recruit three 'lost dwarves', who look very similar to characters from The Lost Vikings on SNES.
Violent, pedestrian-squishing racer Carmageddon was only allowed to be released in the UK with zombies instead of people roaming the streets. In the Indian version, the cows were removed, and it was banned altogether in Germany.
In Germany, copies of Medal Of Honor: Frontline had to be reprinted because there was a swastika on the back cover. The developers also had to go back into the game and take out all the Nazi flags and other paraphernalia.
In the first Fallout, if you create your own character with less than 4 intelligence you can't converse with anyone; your only dialogue options are various grunts or other guttural noises. This makes the game insanely difficult to finish.
Thanks largely - we hope - to being bundled with a Wii-mote, Wii Play has sold around twice as much as Halo 3, shifting some 16 million copies.