Marilyn Manson Triptych Concept Albums (and Chapter 10 of the Holy Wood book):
The Worm/Little Horn/The Disintegrator (The Antichrist Superstar) - Gryffindor (rare fallen example, since he's a tragic hero that became a villain)
Omega - Hufflepuff
Alpha - Gryffindor
Coma - Ravenclaw (going by the book)
Adam - Gryffindor
The President - Slytherin
Batman: Arkham games
Batman - Slytherin (rare heroic example, using money, fear, intimidation, violence and manipulation for good)
The Joker - Slytherin
Harley Quinn - Ravenclaw
Ra's Al Ghul - Slytherin
Oracle - Ravenclaw
Robin - Hufflepuff
Alfred - Gryffindor
Mayor Sharp - Slytherin
Mr. Freeze - Ravenclaw
The Penguin - Slytherin
Catwoman - Gryffindor, in this universe, though she'd never admit that.
Harvey Dent - Gryffindor
Two-Face - Slytherin
Poison Ivy - Ravenclaw (brilliant, and not really evil)
Hugo Strange - Slytherin
Scarecrow - Slytherin
Riddler - Ravenclaw (while this Riddler is much more evil than usual, he's even more smug about his intelligence)
Bane - Slytherin
James Gordon - Gryffindor
Vicki Vale - Hufflepuff
Nightwing - Ravenclaw
Azarel - .....
Halo:
John-117 - Gryffindor
Cortana - Ravenclaw
Captain Keyes - Gryffindor
Andrew Del Rio - Slytherin
Miranda Keyes - Gryffindor
Dr. Halsey - Ravenclaw/Slytherin tossup
Linda - Gryffindor
Kelly - Gryffindor
Kurt - Ravenclaw
Noble Six - Hufflepuff
The Librarian - Gryffindor
Bornstellar-Didact - Gryffindor
Didact - Slytherin
Mendicant Bias - Gryffindor (tragic hero variant)
343 Guilty Spark - Ravenclaw
Gravemind - Slytherin