So many to choose from, I will pick a couple. Recently, a good friend of mine and myself beat Ghouls and Ghosts Twice on the Sega Genesis. It took us a couple of hours, but it was fun to play though a game that is rarely seen at its true ending.
Also, about 6 years ago, I played though Magician Lord with some of my friends on my Neo Geo AES. The ending is extremely brutal, and it was a very savory moment to see the ending of that game.