I know this is possible because I've seen it. I don't know if these are similar effects but here goes:
1. There is a scene near the end of the last Matrix movie when Neo goes to Sentinel city. There are millions of sentinels flying around and then they mesh to form a face. Is that something that can be done within Maya without causing instant insanity? Seems like it's basically a displacement map of someone talking
2. I recently saw a commercial for a new video game (strangely enough, The Matrix also, I believe) whereby this giant creature grabs objects and attaches them to itself to form body parts (e.g., parts of buildings to form its legs, a bus forms part of the torso, etc.). Unlike the first scenario, I suppose that could just be a matter of placing those objects into the appropriate position? Nothing special going on?
My interest is primarily with the first item. I think I could also apply that info to smoke, a cloud, etc.
Creating a large object ('gestalt') out of many smaller objects ('components') can be done pretty straightforwardly with particle instancing.
There are several steps involved. First, create an object which has the shape you are going to want the gestalt to approximate. In your Matrix example, that would mean modelling and animating a face.
Next, create a particle object and make that first object a goal for those particles. This will cause the particles to move towards the goal object and arrange themselves all over the surface. There are various techniques and tweaks that can be used to change the flavour of it.
Next, create the object(s) which you want to be the components. Instance them to the particle object, and that's that: a copy of the object(s) will follow each particle around, so the final render will contain hundreds or thousands of those objects exhibiting the animation of the particles--which in turn will be influenced by the animated object (which of course you will hide, and not render).
Read up on particle instancing to figure out how to randomize and animate the component objects, and read up on particle goals and dynamic fields to add other behaviours to the gestalt.
This is a pretty major sort of project, so my response is very general. If you're planning on tackling it, you can feel free to post specific questions.