I agree - we certainly need per-game controls for N64 (and PS, and any other consoles that have as many or more buttons than the Xbox controller).
You mention Goldeneye - do you remember that when playing Goldeneye (and Perfect Dark) on the N64 you could use two N64 controllers, one in each hand? That way you had proper dual analogue control for both looking and moving. It would be excellent if N64 emulator authors could have their controller configuration sophisticated enough to map one Xbox stick to one N64 controller, and the other stick to another controller, to have proper Halo-style dual analogue for Goldeneye and Perfect Dark ;-) Lovely.
pelago