The way I have the buttons set up for use with my N64 emulator goes as follows:
Analog Stick: Up, down, left, right
D-Pad: I, k, j, l
C Buttons: w, a, s, d
A: X
B: C
Z: Z
L: Ctrl
R: Space
This works really well for me, and most of my friends use the same configuration.
Additionally, I hate using WASD for movement unless it's a game that uses a mouse, like FPSs.