Simbeeotic is a simulator geared toward modeling swarms of micro-aerial vehicles (MAVs). It was originally developed as part of the RoboBees project at Harvard University. Simbeeotic provides a 3-dimensional virtual world in which swarms operate. The simulation is backed by a physics engine that handles the kinematics of the objects in the world, including collisions between them.
Information on installing and using Simbeeotic can be found on the wiki.