Are there stencils for thermal paste/grease?
A stencil could be used as Scott mentions, or a "silk" screen with adequately large mesh for the viscosity of the thermal grease. I put "silk" in scare quotes because most screens these days are polyester mesh. 



I have not used these for this particular purpose, but I have done more than enough silk screen printing to know it would be no problem to print arbitrary patterns of thermal grease on the flat surface of a heat sink (for example, 12 TO-220 package outlines could be printed at once). 

The problem comes in if the surface has any protrusions (such as fins) which could interfere with the screen or the screen frame. 

In the case of stencils, the viscosity is similar to solder paste, so printing should be similar. You could create a gerber file for the stencil maker as you would for a PCB layer. In the case of a screen, they normally work from graphic arts files such as Adobe Illustrator or PDF.