OpenGL Rendering Modes / Using a Color Mask

I would like to set Unity3D to draw in an overlay mode where it draws over other non-unity windows. This is for using unity output behind other text / images created by another application.

I am sorry I do not know the proper vocabulary. But this is like setting VLC Media Player and/or Media Player Classic to render in an overlay draw mode (which disables screen capture) but allows setting the background color of another app to 0x00F / 0x001 respectively so that the rendering from VLC or MPC will draw over the 0x00F/0x001 mask while leaving the other text alone, thus blending video with anything else very quickly.

The word you seek is embedding (imbedding)

This will help you:

The mode you seek is called, "Hardware Overlay" Wikipedia. And although not officially supported by OpenGL (too much hardware abstraction) on MacOSX it may be supported in later versions by QuartzGL, OSX's on flavour of OpenGL. Most Windows applications use hardware overlay through a DirectDraw layer.

Enable QuartzGL for the application using the application's plist file, then set the mode to hardware overlay. In OSX the color is typically a shade of green.