I would think it's all in preference of comfort and the game. I like the nunchuk in the Zapper handle so if I need to do something, like grab my drink real quick, I don't have to fumble with the nunchuk.
Resident Evil: Umbrella Chronicles= reuc
Super Mario Galaxy= SMG
MSC= mario strikers charged
MP3:C= metroid prime 3: corruption
MoH:H2= Medal of Honors Heroes 2
LoZ:TP= Legend of Zelda: Twilight Princess