Another awesome NES game that wasn't very popular was StarTropics: an action-rpg where your primary weapon was a yo-yo. Funny dialog and minor puzzles in the rpg mode, fun gameplay and hidden stuff in the action mode.

I also have to mention King's Bounty, the predecessor to the Heroes of Might and Magic series. You lead an army of creatures around four continents capturing villains for bounties, and clues to the location of some hidden sceptre, the finding of which constitutes winning the game. Some interesting bits reappear in HOMM, like the fact that creatures from the same terrain type get along better together. Some features are unique, like your leadership rating, that limits the number of creatures you can safely control, and the fact that you have to pay out money to your army weekly, or they'll desert. This made some creature types (like orcs) more cost-effective than other seemingly better ones (black dragons). KB came out for PC (dos) and Genesis.