A list of (almost) every non-playable 3rd party IP in Smash:
James Bond
Perfect Dark
SimCity
Tetris
Rayman
Bit.Trip
Shovel Knight
Bomberman
Shantae
Rabbids
Monster Hunter
many Namco universes, most notably Tekken, Mappy, Tower of Druaga and Galaxian/Galaga
Virtua Fighter
assorted Mega Man spin-offs
Tales of
and here's some select crossovers they've been in:
Tetris has crossed over with Mickey Mouse, Puyo Puyo and Cardcaptor Sakura
Rayman has crossed over with Assassin's Creed, Beyond Good And Evil and Splinter Cell
Bit.Trip has crossed over with No More Heroes and Bubsy
Shovel Knight has crossed over with Yooka-Laylee, Octodad and VVVVVV
Bomberman has crossed over with Transformers, Licca-Chan (the Japanese counterpart to Barbie) and Adventure Island
Shantae has crossed over with Blaster Master
Rabbids has crossed over with SpongeBob SquarePants, Fairly OddParents and Teenage Mutant Ninja Turtles
Tekken has crossed over with PaRappa the Rapper, God of War and InFamous