Good things for prototype systems:

• Based on a high level programming language
• Smallness
• Cross platform
• Mature toolchain to simplify asset generation
• Ease of moving to a production engine

Advantages:

• Low tech forces focus on the ideas - this is really important I think
• Ease of running/viewing/playing
• Use of commonly installed things - web browser/flash plugin, blah.

Disadvantages:

• Have to run everything in a virtual machine/interpreter so a bit slow
• Not much in the way of graphics features (not really a problem for prototyping)
• 3D possible but is not really the focus in these systems, so it can be awkward

processing → http://processing.org/

haxe (compiles to swf/js/…) → http://haxe.org/

Advantages:

• Prototyping in the same system you produce the game in saves time (arguably)
• You can have access to the same features in the prototype as a final game

Disadvantages:

• Complexity kills creativity - game engines tend to have a lot of complexity
• Have to install stuff, more chance of platform incompatibility

Blender game engine → blender game engine notes

• Blender is a good option as it's the same tool used to create the artwork - there may already be a familiarity
• Scripted in python which is a good prototyping language

Fluxus → fluxus notes

• Fluxus is scripted in Scheme which is a good prototyping language
• Deliberate perversion to games industry 'best practices'
• Not working on windows
• Difficult to install - big minus points
• Works best for fast graphics prototyping at this point (rather than gameplay prototyping)
• Frisbee (functional reactive programming/animation in fluxus) might provide a much better, smaller, more creative way of writing games, but it's unproven (to me) and highly experimental at this point.

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 scheme, rather than a complete entity model (I might be wrong these days tho)

Blitz Basic → http://www.blitzbasic.com/ who make Blitz3D → http://www.blitzbasic.com/Products/blitz3d.php

Lots of games written in this, very popular in the indy game dev scene.

Virtools → http://www.virtools.com/

Does online, visually programmed, and looks very suitable - just also kinda expensive.

Unity → http://unity3d.com/

Panda3d → http://panda3d.org/