Good things for prototype systems:
Making games with little time, people or costs → http://www.experimentalgameplay.com/
How to Prototype a Game in Under 7 Days: Tips and Tricks from 4 Grad Students Who Made Over 50 Games in 1 Semester http://www.gamasutra.com/features/20051026/gabler_01.shtml
A good rapid prototyper would realize that failure is ok! That's what prototyping is for, so go crazy! If you fail, there will be dozens more, and chances are, you'll learn something anyway. By embracing the possibility of failure, rewarding experimentation becomes possible.
Eg: plant game
processing → http://processing.org/
haxe (compiles to swf/js/…) → http://haxe.org/
Blender game engine → blender game engine notes
Fluxus → fluxus notes
PyGame → http://www.pygame.org/news.html
Mainly sprite based examples, there are some 3D games, but most seem to involve calling opengl commands wrapped in python, rather than a nice high level entity model (I might be wrong these days tho).
Panda3d → http://panda3d.org/
Free software python based game engine for windows & linux from Carnegie Mellon. Looks really good.
some more notes can be found in the game engines node
Lots of games written in this, very popular in the indy game dev scene.