Game designers don't spend much time thinking about how to implement communication mechanisms in games, but perhaps they should. Non-verbal communication is particularly interesting: it doesn't need localising, it's readily understandable by (most) people and it supports fully mimicry.
The use of the whistle in Shadow of the Colossus is a great example. Whistle for your horse, or to attract the attention of a colossus - it adds greatly to the feel of the play of this game that one can make a noise.
Similarly, the horn in Mercenaries is a nice touch. Beep your horn to get people to board your vehicle (just like in real life!), or when you are disguised, beep your horn to let allies know that it's you. Simple, logical, and supporting mimicry. Easily the best part of the design of this game.
The ocarina in The Legendof Zelda: The Ocarina of Time is also interesting, here using music to communicate. This is perhaps under used, but the moment when one reveals oneself to Epona on the basis of a particular tune is truly inspired.
I look forward to a game with a 'wave' button, in which the flailing of a hand becomes an element of play.
Anyone have any other examples of non-verbal communication in games they'd care to share?