If you have ever dreamed to see a chip operating at a transistor level, take a look at this crazy project presented at Siggraph this year: a transistor level simulator of the 6502 CPU (that was powering the Apple 2) !
Greg James, Barry Silverman, Brian Silverman who are leading this project built the simulator by reverse engineering the chip from high resolution die shots they used to reconstruct the full polygon model of the chip circuits !

They provide the simulator as a javascript applet you can use to program the virtual chip and see the circuits operating : http://visual6502.org/JSSim/index.html 

The Siggraph talk can be found there: http://visual6502.org/docs/6502_in_action_14_web.pdf