Earthbound, Secret of Mana, EVO: The Secret of Eden, Paladin's Quest, Super Ninja Boy, Chrono Trigger and several others for my SNES collection. After so many years, my SNES was starting to crap out and the games themselves were starting to be a little dodgy, so I had to sell what I could and throw the rest out. D: ESPECIALLY EARTHBOUND.
On the flip side, one time I sold my original copies of Suikoden I and II. Then I realized what a BAD decision that was. Luckily later on I managed to buy working copies of both of them again!