For some reason, I find it rather uncomfortable to use my middle fingers for pushing the L and R buttons / triggers. So, I have the thumbs on the analogue sticks, index fingers on the L & R buttons, and everything else holding the bulbous bits at the bottom.
Of course, it changes when using something completely different. For the N64, I'm seeing if its easier and more comfortable to hold it as I usually do, or to hold the middle bulbous part and control the analogue stick with the thumb and the Z button with the index finger.
And of course, for gamepads, there's really only one main way - thumbs on d-pad and buttons, everything else holding the sides.
*EDIT*
I forgot joystick, but really, how many ways can you find to hold a vertical stick attached to a base?