Don't know if it's been mentioned, but Just Breed for the NES.
The recent fan translation is excellent, though spell names take some navigating, and it has what I feel is a great combination of gameplay and storyline. Well, let's face it, the overarching plot is cliche, but where this game shines is the characters. It has wonderful characterization.
The basics... Just Breed is an SRPG by Enix, it was their final game released for the NES and it is the largest NES game ever made.
If you want to have a look at it, take a peek at this walkthrough but be aware that it, of course, contains spoilers. Just Breed is definitely a lost gem, easily the best SRPG for the NES in my opinion and one of the best RPGs of its era.
Another old overlooked favorite of mine is Nightshade for the NES. It's a very unique combination of action, adventure, roleplaying, and puzzle. The plot is fairly unique for its era, it stars an 'up and coming superhero' who is investigating the death of the city's previous superhero while exploring the city and fighting crime. One of my favorite features is that each time the main character 'dies' in battle, he awakens to find himself in a progressively more difficult trap (a puzzle); 1960s Batman sort of deals. It's still one of the most unique ways of handling 'multiple' lives that I've seen in a game. Eventually the traps got far too difficult for me to escape, at least. Very difficult game that challenges in a lot of ways but it was a lot of non-linear fun.