You might also want to take a look at my JS games.
Bifurcation Diagram of the Logistic Map - simulates thousands of random populations (which grow according to a logistic equation) over time to produce the bifurcation diagram, showing wildly different results depending on changes in the equation's parameters.
Boids - a simulation of flocking/schooling behavior (e.g. birds, fish)
3d engine - a real 3d engine. It uses z-buffering, so mutually-overlapping objects render properly. The z-buffer implementation uses an optimization I came up with that saves paint operations. I wrote this before WebGL was created.
Rollercoaster / Space flight - riding a rollercoaster, or chasing a TIE fighter to the Death Star. This is a pretty complex engine, supporting arbitrary camera and object transformations, and simple triangle clipping. The animation uses catmull-rom splines. This was also written before WebGL was created.
Starfield - flying through a starfield. The 3d effect is a crude illusion (no fancy math).
Substrate - an approximation of a material cracking, which produces really nice patterns.
Raytracer - a raytracer. It's buggy and incomplete, but works well enough to render spheres.
Dewdney's Voters - a simulation of easily-swayed voters. Each voter randomly picks one of its neighbors, and switches its vote to match. Which party will win?
Popsquares - artsy pulsating colors.