Scrubs (Double Dr. Mario)
Jurassic Spark (Pika and Yoshi)
Apes and Capes (DK and Mario)
Barbequed Bananas (Bowser and DK)
Knee Surgery (CF and Doc)
Shock Therapy (Pika and Doc)
Stomp the Yard (Ganon and CF)
Animal Crackers (Fox and DK)
Here's your tip, keep the change (Marth and Mario)
Transformers (Zelda and Sheik)
Sausage, Egg, and Cheese (G&W and Yoshi)
Handicapped Parking (Y link and Roy)
Suicide Pills (CF and Doc)
I can't think of the other ones atm.
If we're talking character specific, here's some good ones:
Sugar 'n' Slice (Peach with Marth/Roy/Link/Y. Link)
Monkeyshines (DK with space animal)
Super Slash Bros. (any combination of Link, Y.Link, Marth, Roy)
Speed of Lightning, Roar of Thunder (Falcon with Pikachu)
Bomb Squad (any combination of Yoshi, Link, Y. Link, and Samus)
Younger Generation (Y. Link, Pichu)
Elder Generation (Link, Pikachu)