DeskProto - Seems great for proto stuff. Not too expensive either.
Vectric - Offers several different CAM packages from 2D to 3D. Cut 2D is interesting for the mill.
CNC Controller:
Mach3 - Works and very popular, but I find the interface to be terrible. Also has issues with running on a laptop, which I have addressed and resolved here.
EMC2 - Linux based CNC controller. Supposedly has superior parallel port communications.