-2nd wiimote
-2nd nunchuk
-classic controller
-3rd wiimote
-4th wiimote
-2nd classic controller
-3rd nunchuk
-4th nunchuk
-3rd classic controller
-4th classic controller
Thet priority list should do for most cases, although it does not include GameCube controllers and is balanced for a priority on Wii games, not VC games.
Best Controller for VC games:
NES: Wiimote, Classic Controller (CC has better placement of start/select, wiimote is better with A and B)
SNES: Classic Controller
N64: Gamecube Controller (close second: Classic Controller)