I have vivid memories of autonomous mode in 2008. In overdrive the autonomous mode involved driving straight and then turning left (AND NOTHING ELSE!). Of course halfway through the Florida regional our robot decides it wants to be unique and starts turning right in autonomous mode (which I will point out, there was no function ever written in code to turn the robot right). At first I thought we had achieved robot sentience and that the robot was now programming itself, but then we discovered the broken encoder.
Another favorite is from this year. The first couple times we downloaded the code we kept getting an 'out of memory' exception. It had me scratching my head for a while until I discovered an exciting (and accidental) recursive function call written by one of the programming students. The code looked something like:
public void moveArm(double val) {moveArm(val);
}