Depends on your tastes and how much you're willing to spend.
If you loved the N64 controller, then Toasty's suggestion is dead on. If you didn't, but prefered the PSx styled controllers, you should go with that (since they have adapters for almost EVERY controller type). If you wanted to, you could use the X-Box controllers, those are really great for playing your games AND offer you all of the buttons in a very decent format for gaming. Hell, you could even try the GBC controller, because that's pretty decent too.
In the end, it's always best to go for what you're comfortable with and what you can afford. So in the end it's up to you what controller to get. Me? I'm using a Playstation 2 Dual-Shock controller with a Radio Shac USB-to-PSX adapter. It works great, and I have perfect rumble function and everything is smooth.