I don't have a example of a old game off the top of my head but I can give you nitendo and a starfox game mod, nitendo can't do anything with the license thats half decent so there's no reason to touch a fan made game meanwile they ruthlessly shut down anything that boards competition to there top franchises like zelda and mario.
I wouldn't place money that they wouldn't shut down a fangame to Metroid or Star Fox - they axed a Metroid fan remake back in September, and last year a Star Fox fan cartoon got canned. They seem to be sporadic for what gets the ax.
Pokemon Uranium is the most recent one I can recall, but Pokemon is one of their bigger franchises. But, for example, Square Enix has squashed two fangames based off Chrono Trigger, where the closest thing they have done with the property is the DS port.