I share H_C's opinion. Keep the consoles games for couch playing, on their designed-for controls. Just like Arcade games should use the controls they were designed for (Time Pilot or Gyruss with a Spinner is just wrong - sorry lew).
But it's your life, do you man.
I would suggest a Toodles' MC Cthulhu board and build your own RJ45 cables, and just get controller adapters for the consoles that it doesn't support.
First off, nothing I'm doing prohibits one from taking the console, hooking it to the tv, sitting on one's duff and playing with an original controller for hours in an immobile state. I'm just adding the ability to hook up to my control panel if I want to.
There is no way you could convince me that clayfighter 2 would be better on a snes paddle than through my control panel, and that emulating it on pc it is just as good a playing on console, or a composite cable looks as good as RGB.
You also can't convince me that MvC2 on dreamcast is better on a DC controller, or an emulator.
I could go on, I have my reasons, let's keep it technical. killer advice on the cthulu though, I have seen some about this already and i am still leaning towards 2 hacked gamepads and a basket full of adapters. My concern with it is having to have wires for each system linked to it all at once AND if I have it connected to a pc and a console at the same time does the console get zapped?
Any more advice is certainly appreciated. Thanks all!