This is G3's rather inclusive stage list. This is the default list for tournaments, events, and gyms. If you disagree with any of the classifications please post here to say why.
Neutral:
Yoshi's Island [Brawl]
Battlefield
Smashville
Final Destination
Pokémon Stadium 1
Counterpick:
Lylat Cruise
Halberd
Castle Siege
Delfino Plaza
Brinstar
Frigate Orpheon
Rainbow Cruise
Jungle Japes
Pirate Ship
PictoChat
Pokémon Stadium 2
Norfair
Luigi's Mansion
Distant Planet
Banned:
Green Greens
Yoshi's Island [Melee]
Port Town Aero Dive
Hanenbow
Mario Circuit
Onett
Corneria
Big Blue
75m
Green Hill Zone
New Pork City
Rumble Falls
Shadow Moses Island
Summit
Mario Bros.
Flat Zone 2
Bridge of Eldin
WarioWare Inc.
Spear Pillar
Skyworld
Temple
Mushroomy Kingdom