Since I have had no luck finding such a list online, I plan to start a new Apple TV page that will cover the various multiplayer and 3-D games.
Multiplayer implies more than one player at the same time. There is no category for this in the app store, so unless the developer puts that word in the description, you won’t find these games with a search.
I was very surprised to find that the new 4th generation Apple TV supports 3-D content. The Pangea Software games (some of which I’d played on the Mac years ago) are the only ones I’ve found so far that work in 3-D. Really neat.