... in video games, that the authors regret putting in them.

Deus Ex was of course ripe with conspiracy theories and whatnot, but that's because of the X-Files and because you were supposed to take it as a parody.
Same with the gnome & half-ogre quest in Arcanum where you uncover a conspiracy that gnomes in the world of Arcanum run a secretive operation to abduct Human white women and have them raped by ogres, so that they could then raise the half-ogre babies as their obedient golems.

Both of these were designed by brave Jewish men, Warren Spector and Leonard Boyarsky respectively. They both said they regret putting them in the game, they only put them in their games because it was a different vibe back then. Deus Ex's Twin Towers were missing long before crazies blamed Israel for 9/11 (Warren mentioned this specifically), due to a technical limitation in the engine (it would take too many resources to have the twin towers in the 2D sprite in the skybox). Likewise, Leonard said that Arcanum came out before the association between Jewish folks and gnomes, or before the left correctly recognized that orcs/ogres and whatnot are quintessentially based on Black racial stereotypes.

It's so sad.