Gravity changes only take effect when you click Start. (This is indeed allowed while the simulation is running, however.)
Elasticity changes take effect when the cursor is in any elasticity box and you hit the Enter or Return key.
Reloading the web page will quickly clear all balls and graphs.
Selecting Lock Stopped Graphs will stop a graph from scrolling once its ball comes to rest. This will cause multiple graphs to line up on the right rather than the left, to interesting effect.