As long as assets, code, anything else, including trademarks are not used within the game or to create the game (other than reference) I'm pretty sure it's fine.
As soon as you call it Super Duper Mario Sisters or Warfield: Modern Battlefare though, people are going to take notice.
I feel confident that I could emulate say.. Terraria without getting legal issues, as long as I didn't use any of their assets, code or tried to leach off their names.