If you are going to go with a USB gamepad, I would get a Saitek.
I have two
Saitek Dual Analog Gamepads, and I use them for all consoles, including N64. It works very well, and I'm very happy with it. (Just to note, the one linked above is not the exact one I have)
However, if you're up to it, get an adaptoid to put an N64 controller on your machine. Nothing beats it.
But, the Saitek is useful because it has shoulder buttons, as well as six buttons on the front in addition to others. The six buttons on the front are in a good configuration for sega games, and also work well as the C buttons on an N64 controller.
As far as brophog's comments, I wouldn't think it applies to N64 or other complicated console controllers.