Almost every system has a few cab friendly games, but for the games like Super Mario 3 and stuff where a controller is just so much better, I just stuffed two ps3 controllers in the coin collector door of my cab and leave it unlocked. They are mapped to mimic the 6 button controller layout I have setup on the main controls, and depending which cord you plug them into they can also be used as player 3 and 4 (I have a 2 player fighter layout) for most systems. (super fun for tmnt/simpsons).
For the N64 though, some games you just simply cannot map very good with anything but a N64 controller. I have considered purchasing a couple of them with the usb adapter thing on them from a few different websites, but I haven't been able to pull the trigger on it. The analog stick on the N64 controller is notoriously short lived. Fortunately, a lot of gnarley games can be played fine with the 6 button arcade layout (NFL Blitz, Crusin' USA, Mario kart, KI Gold, MK Trillogy). On an added note, I originally started out by just adding as many games as humanly possible to my machine. Wish I would have added in smaller batches and did more tests, Because, now I'm stuck weeding out the bad ones/trying to get cool screen shots, and it totally sucks.
Sorry for the late post, I just thought this might help somebody one of these days.
