Secret of Mana is technically superior imo, and set a pretty high bar for graphic standards for a long time. It's still one of those games that is used as a reference for aspiring pixel artists. Not only are the tiles really nice, but the sprites and animations are amazing as well:
http://images.nintendolife.com/screenshots/23935/large.jpg (Unsupported image host)http://www.gamers-tavern.com/assets/screenshots/sd3_06.png (Unsupported image host)http://lparchive.org/Seiken-Densetsu-3-%28by-ddegenha%29/Update%2020/6-SD3_19_3.png (Unsupported image host)http://lparchive.org/Seiken-Densetsu-3-%28by-ddegenha%29/Update%2002/36-SD3_2_36.png (Unsupported image host)http://lparchive.org/Seiken-Densetsu-3-%28by-ddegenha%29/Update%2016/24-SD3_15_17.png (Unsupported image host)

Another honorable mention(and somewhat unknown game) is Tales of Phantasia. Not technically pretty, but in-game everything is so fluent and appealing to look at, sadly screenshots don't do it justice, though:

http://s.emuparadise.org/Super%20Nintendo/Snaps/Tales%20of%20Phantasia%20%28J%29.png (Unsupported image host)http://www.mobygames.com/images/shots/l/53201-tales-of-phantasia-snes-screenshot-no.gif (Unsupported image host)http://www.mobygames.com/images/shots/l/53196-tales-of-phantasia-snes-screenshot-nice-shadows.gif (Unsupported image host)http://www.mobygames.com/images/shots/l/53193-tales-of-phantasia-snes-screenshot-nica-attention-to-detail.gif (Unsupported image host)http://www.mobygames.com/images/shots/l/53198-tales-of-phantasia-snes-screenshot-forest.gif (Unsupported image host)http://www.mobygames.com/images/shots/l/53200-tales-of-phantasia-snes-screenshot-there-are-many-really-beautiful.gif (Unsupported image host)

Zelda is of course really appealing in its simplicity, but it's hard to overlook some really bad flaws the game had in some of its graphics. I feel like the screenshots should have shown some variation(such as Dark World, which has a better tileset I think, personally).