Console Emus - Plugging in USB Controllers without Remapping?

[JdotFite]

While searching this topic, I came across drventure's Controller Remap software.  It sounds awesome and is so close to what I am looking for.  Does something like this exist for other emulators, besides MAME?

I just finished a mini weecade build and I am using the ZD encoder for a 1 player control panel. I would like to be able to play NES with my control panel, but also have the ability to plug in my rewired NES usb controller(s) and be able to play without remapping all the keys.  Same would go GEN/SNES/etc. Is this something any of the emulators have built in or has someone made a utility similar to Controller Remap for this sort of situation?  I hope this is possible.

Thanks,
Justin