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 develop for saves time
• 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
• Working on it…