Good idea for a thread, Wholly. I recall Shadow Warrior being dinged for potentially offensive stereotypes. Certainly 9/11 changed a lot of game development, from the Twin Towers and building collision detection take out of Flight Simulator series to whole projects being re-tooled or reconsidered. At the risk of inciting Lizard King's weird accusations that I'm hysterical or hypocritical or whatever, I'm glad to see Six Days in Fallujah had a hard time getting a publisher after the developers' blundering attempts to drum up publicity.
Most recently, I was surprised that Ubisoft selected Jenny McCarthy as their celebrity face for a fitness game. By selecting her as a health and fitness authority, they're implicitly endorsing her vocal stand against childhood vaccination.