Holy revived thread batman!
Well, after doing some searching around, ive decided to use chinese knockoff n64 controllers with usb ends. works pretty well. the only issue with this of course is nemu hates usb controllers being unplugged/plugged in so anytime i want to use them, i have to go into the emulator and set joy1, joy2, etc. but it saves the profile. just a headache before playing the games.
initially i used x360 controllers, but im finding it definitely does not have the same feel when playing sega genisis/cd/saturn. so no bueno, we end up just not playing them because of it.
As for the 4 button vs. 6 button layout, i have finally come to a solution to that. most of the emulators i can set the config.ini to read only after configuring the controllers. i intend to use PS3 controllers. why ps3 you may ask? well with ps3, the wireless 6 button controllers are available (fightpads, etc.) and all i need to do is just turn them on and sync them. and when i get tired of those, throw them on the charger, let them disconnect, and sync up the standard controller. no wires, no mess, and they completely resemble the sega saturn controller. the gf will just have to get used to not using the x360 controllers :-P.