Because I haven't written anything on here for a few months and this list needs continuing.
(Key: FAV - Favorite; HM - Honorable Mention; NO - Notable Omission)
FAV: Super Contra (NES)
Everything that was great about Contra, but now enhanced with far better music, level variety, and speed. The top-down segments for navigating bases are better than the original's weird over the shoulder parts.
HM: North & South (NES)
A surprisingly good attempt at an educational game that ends up being more fun to mess around with than learn from. North & South is like turn-based strategy meets real-time combat, but on ancient hardware. You play out the American Civil War, either from the Union or Confederate perspective, capturing bases, gaining funds, and dealing with random thunderstorms and Indian attacks. It's difficult to explain why this game is cool without having people play it and see for themselves.
HM: Super Mario Bros. 3 (NES)
This game is so many times better than Super Mario Bros. and the oddity that was vegetable-plucking Mario 2 that it makes up for Japan not localizing the real Super Mario Bros. 2 until Mario All-Stars on the SNES. Mario 3 is better than Lost Levels anyway. This game has some of the best level design on the original NES, especially for a platformer. It has great pacing, variety, and a wealth of secrets that keep it from growing dull throughout the entire adventure. Also, the powerups were awesome. Even the frog suit. EVEN THE FROG SUIT.
HM: Super Mario World (SNES)
It provides the same degree of improvement on Mario 3's concepts that Mario 3 provided for the series as a whole. World is in many ways just like Mario 3, but better at what it does in every single way. I played a lot of this game when I was younger, and I will always appreciate its less-is-more approach to game design: Polish and improve the ideas you have, don't veer too far from your core.
NO: Final Fantasy (NES)
A great example of a game that laid down the foundation for far superior games, FF1 is another cool idea that is better remembered for reorganizing existing gameplay concepts in an innovative way rather than being a good game itself. There are three things it got right: Exploration (open worlds are awesome), Strategy (combat based on careful use of character abilities and items, not reflexes), and Interface. Final Fantasy is a lot more appealing to look at and less extraneous than the early Ultima games, despite having less depth. It's a good example of streamlining features towards a better game experience.
NO: Mega Man 3 (NES)
Most people I who mention this game either consider it to be superior to be either the peak of the original Mega Man series, or the point at which it began to go downhill, being good but not contributing as much as MM2 did. The level design in this game is almost identical to MM2's layout, because Mega Man is one of the most formulaic franchises of all time. I will always consider the original 6 Mega Man games to have inferior gameplay to the early X series, but the original games were more balanced in design. Mega Man 7 is a strange beast that will be addressed in the future.