Clock Tower is not only the best true horror game on the Super Nintendo, it's one of the best horror games of all time. This iconic point-and-click horror adventure game was the first entry in what went on to become a classic franchise with sequels on the PlayStation 1 and PlayStation 2. Taking inspiration from Italian horror movie maestro Dario Argento, specifically the film Phenomena AKA Creepers (seriously, this is almost a straight-up adaptation of Phenomena in 16-bit video game form, right down to the main character clearly being modeled after Jennifer Connelly), this creepy title has you trying to escape a mansion while being hunted by the game's terrifying signature villain Scissorman. Along the way you'll uncover some horrifying scenes and hopefully rescue a few of your friends in the process. A true classic, Clock Tower is highly recommended and is a must-play for every fan of horror games.
Unfortunately Clock Tower was only released in Japan for the Super Famicom back in the day, but it has received a great fan translation and English-language reproduction cartridges for the SNES are plentiful on eBay.
Super Castlevania IV
Castlevania Dracula X
Musya: The Classic Japanese Tale of Horror
Super Ghouls 'n Ghosts
Zombies Ate My Neighbors
Laplace No Ma (Laplace's Demon)
Shin Megami Tensei, Shin Megami Tensei 2, Shin Megami Tensei If...
Adding to the list of horror games that were only officially released in Japan for the Super Famicom, the Shin Megami Tensei series for the Super Famicom is an interesting and unique first-person horror RPG from Atlus. Combining strong horror elements with classic dungeon-crawling RPG gameplay. The games were impressively non-linear for their time and feature a more mature story atmosphere than most 16-bit games. I'm lumping them all together here because they all play more or less the same, but they're all worth checking out if your looking for some interesting horror games for the SNES. Shin Megami Tensei, Shin Megami Tensei 2, and Shin Megami Tensei If have all been translated to English by fans so they're fully playable and English SNES reproduction copies are available to purchase on eBay.