Honestly I am very picky when it comes to the controller.
To make an example, in order to play mame games"the way they where ment to be played" I cashed out 150 USD to get an X Arcade controller, and if I may ,it was well spent money !!
But for the N64 emulation at first I used a PS2 dualshock controller , which was connected to my PC via an adaptor called PC Magic Box( around 14-15USD) from link-sang.com, but as you all know the analog function of the dualshock is nowhere close to the feel of the original N64 Controller,plus it's a little tough to map all the buttons, because the right analog stick doesn't exactly replace well the C-buttons.
I got eventually another adaptor, still from link-sang, called Trio Linker Plus($19 I believe), and it works with DC,PS2 and Game Cube controllers plus other peripherals like official steering wheels and dance mat,and it supports the RUMBLE feature!!
I have to say I am really satisfied with the GC controller, it's very responsive, just as sensitive as the original N64 one, and plus the buttons layout adapts very well to emulate all the buttons required.
If you already happen to have a GC controller in your house, then you can't beat this set-up !!