There are some good suggestions, but I'll throw a few different options down as well for the upcoming SNES retroactive:
Metal Marines - Interesting strategy game where you build base defenses, and then command airstrikes against an opponent on a nearby island. Not a true classic but maybe an interesting game to discuss. General strategies, what you do/don't like, what impact it has had on other games or genres that we still play (the popular tower defense genre comes to mind)... Nice that it's password based, so people can skip around levels if they need to.
Ogre Battle: March of the Black Queen - In honor of Ogre Battle 64 getting mentioned as a "top 3" game in the podcast, why not explore this deep strategy game to see how it holds up today?
Super Mario RPG - A popular and well-received game... so how come Nintendo's flagship RPG switched to Paper Mario and never went back? What characters did you like/despise?
DoReMi Fantasy - Milon reappears, but the gameplay is (thankfully) much better than in Secret Castle in this old-school platformer. What better way to give newer gamers that "import" feeling, especially during cut scenes?
Legend of the Mystical Ninja - Goemon to the rescue! An oddball adventure that includes solid (if silly) multiplayer and unusual minigames to break up the action. A cult favorite that more people should try playing, this game always reminded me of the much lauded River City Ransom somehow.