Well, you could buy an USB controller, that's a great solution because playing PJ64 with the keyboard sucks horribly. I myself use a Genius MaxFire Blaze 2, it is an usb controler that can also connect to a PS2, and as you may have guessed, a PS2 controller has more buttons than the N64's.
If not, try this recommended keyboard settings:
a=z, b=x, z=c, l=a, r=s, start=enter, C-up=y, C-left=g, C-right=j, C-down=h
for digital pad/analog stick use the normal arrow keys.
You can also save and load settings for other games