I've never really gotten into the Harry Potter books and films, but from what I remember:
Gryffindor: The hero's house
Hufflepuff: The butt-monkey's house
Ravenclaw: The anti-hero's house
Slytherin: The villain/nemesis' house
Anyway:
Puyo Puyo universe:
Arle Nadja - Gryffindor
Schezo Wegey - Hufflepuff
Rulue - Ravenclaw
Satan - Slytherin
Draco Centauros - Slytherin
Witch (yes, that's her name) - Ravenclaw
Amitie - Gryffindor
Sig - Hufflepuff
Raffine - Ravenclaw
Ringo Andou - Gryffindor
Maguro Sasaki - Ravenclaw
Risukuma - Hufflepuff
(Only did select characters because holy shit, there are a lot of characters in the Madou Monogatari/Puyo Puyo series)
Pokémon universe:
"Red" - Gryffindor
"Blue" - Slytherin
"Green" - Ravenclaw
"Yellow" - Hufflepuff
"Gold" - Gryffindor
"Silver" - Slytherin
Kris - Ravenclaw
Kotone - Hufflepuff
Brendan/"Ruby" - Gryffindor
May/"Sapphire"- Ravenclaw
Wally - Ravenclaw
"Emerald" - Slytherin
Lucas - Gryffindor
Dawn - Hufflepuff
Barry - Ravenclaw
Hilbert - Gryffindor
Hilda - Ravenclaw
Cheren - Ravenclaw
Bianca - Hufflepuff
N - Slytherin
Nate - Gryffindor
Rosa - Hufflepuff
Hugh - Slytherin
(Did only the trainers and rivals because, again, really big cast when the whole series is condensed together)
Sonic the Hedgehog (games only):
Sonic - Gryffindor
Tails - Gryffindor
Knuckles - Ravenclaw
Amy Rose - Hufflepuff
Cream - Hufflepuff
Shadow - Slytherin
Rouge - Slytherin
Dr. Robotnik/Eggman - Slytherin
Silver - Hufflepuff
Blaze - Gryffindor
(again, real big cast, and I didn't include the shows or comics)
...and because I swear I'm the only person here who cares about these four and I wanna do them:
Mighty - Ravenclaw
Ray - Hufflepuff
Bean - Ravenclaw
Bark - Ravenclaw