I've been trying to research this and looking through the DP guide as well as all the threads relating to variants. I'd like to make a complete list. I'll list the ones that I've found and everyone else can help add or debunk them. I'll add them to the master list in my first posting.
Million Seller Labels
Donkey Kong Country
Donkey Kong Country 2: Diddy'd Kong Quest
Donkey Kong Country 3: Dixie Kong's Double Trouble
F-Zero
Legend of Zelda: A Link to the Past
SimCity
Super Mario All-Stars
Super Mario Kart
Super Mario World
Super Metroid
Super Star Wars
Tetris/ Dr Mario
Tetris 2
Majesco Re-Releases
Disney's Aladdin
Animaniacs
Aaaaah! Real Monsters
Championship Pool
Contra III: The Alien Wars
Clue
Earthworm Jim 2
Family Feud
Disney's Goof Troop
Jeopardy! Deluxe Edition
Disney's The Jungle Book
Jungle Strike: The Sequel to Desert Strike
Disney's The Lion King
Marvel Heroes: War of the Gems
Megaman X
Monopoly
Ms Pac-Man
Pac-Man 2: The New Adventures
Paperboy 2
Pitfall: The Mayan Adventure
Porky Pig's Haunted Mansion
Scooby-Doo Mystery
Sim City
Speedy Gonzales: Los Gatos Banditos
Spider-Man/ X-Men: Arcades Revenge
Street Fighter 2
Super Battleship
Super Black Bass
Super Castlevania IV
Super Ceasar's Palace
Super Godzilla
Super Off-Road
Super Off-Road: The Baja
Super Star Wars
Super Wrestlemania
T2: The Arcade GAme
Teenage Mutant Ninja Turtles IV: Turtles in Time
Tiny Toons: Buster Busts Loose
Top Gear
Urban Strike: The Sequel to Jungle Strike
Wheel of Fortune: Deluxe Edition
X-Men Mutant Apocalypse
TH Q
Super Star Wars: The Empire Strikes Back
Super Star Wars: Return of the Jedi
2 Releases of Zombies Ate My Neighbors (perceivable by the box only)
John Madden Football 93 has two labels, one that says "John Madden Football" and one that says "John Madden Football '93". The latter has a 1 at the end of the code.
NHLPA Hockey 93 also has two variants, one that says "NHLPA Hockey" and one that says "NHLPA Hockey '93". The latter has a 1 at the end of the code.
Maximum Carnage also has two variants, one in a red cart and one in a gray cart. There was also a Limited Edition Set which came with a comic book and was is a nice case.