It should be obvious from the title alone, but I'll say here: this is only about games that got official paid releases, we're not talking about fan games that got shut down due to legal issues. Anyway to start:
Uniracers
A Unicycle racing game for the SNES that was developed by DMA Design, the same company that'd later become Rockstar North and create the GTA series, and published by Nintendo. After the game was released DMA was sued by Pixar because they claimed the design of the anthropomorphic unicycles in the game bared too much of a resemblance to the unicycle from their 1987 short film "Red's Dream" (guess it doesn't help the game used DKC like pre-rendered 3D graphics). Pixar actually won the lawsuit and Nintendo was forced to stop selling the game, and because of this it can never be re-released.
Too Human and X-Men Destiny
Putting these together because they're made by the same company, Silicon Knights, and were taken off the market for the same lawsuit. What happened was that Silicon Knights made use of Unreal Engine 3 technology in these games but failed to pay a licensing fee to Epic Games, the maker of the Unreal engine. Made worse by the fact Denis Dyack, head of Silicon Knights, once said they were going to drop UE3 from Too Human when he couldn't get the visuals he wanted out of it. In light of the lawsuit it sounds more like Dyack was trying to get out of paying Epic the licensing fee. Epic Games sued Silicon Knights and won, forcing Microsoft and Activision to take Too Human and X-Men Destiny respectively off the market.