Gutted the NES, and Gorilla Glued in some Legos to hold the RPi board in place.
The edges of the RPi slide pretty snugly into the slats on these little grill-looking Lego pieces.
As most people who've dealt with one know, shutting down and turning on the Pi is a pain in the ass. So I got this circuit that will provide the RPi with power when switched on, and then when switched off, run the shut down command, and automatically cut the power when it's finished. I soldered the original NES power switch into the circuit and connected it to the board.
There are also two pins on the RPi, that if shorted, will reset the computer, in case it locks up or something. I soldered the NES's original reset button to those pins, and then soldered in a ground, in parallel with a 180 ohm resistor for the NES LED. It turns out that the NES power switch has a TON of internal resistance, and the NES takes about twice the voltage of an RPi, so the LED was way too dim (even after I removed my resistor). I've since replaced it with one that is wired right into the 3.3V pin on the GPIO. Now the power button, reset button, and LED work with the Pi exactly as you'd expect them to.
Now for the ugly stuff.
I used a Dremel to expand the ports on the back of the NES and purchased adapters for USB (for power), Ethernet, and HDMI. As you can see, it's the first time I've used a Dremel.
Then I used the Dremel to drill out the original NES controller ports to allow for a USB plug to take its place. I bought some SNES USB controllers to use with the set-up.
I had to shave down a few pillars inside the NES to get some of the wiring to work without putting too much stress on any ports. Here it is all wired up. You can also see how I used even more Legos and Gorilla Glue inside to create my "ports" on the back of the console. This photo was taken before I wired (then Lego'd and glued) and connected the ethernet in as well.
And here she is, ready to play.
I loaded it up with Atari 2600, NES, SNES, GBA, and Genesis emulators and ROMs.