Pirates! - The NES port of computer game Sid Meier's Pirates! Was later released on Sega Genesis as Pirates! Gold. And on XBOX with the original Sid Meier's Pirates! title.
Dragon Warrior III - I know the franchise does get quite a bit of respect, but the third is my favorite NES game ever, and I don't see it mentioned as much as the first or some of the later installments.
Rad Racer was an ok clone in 3D of Outrun and 3D World Runner was a Space Harrier clone. Pro Wrestling I did like and would love to see an update. Karnov is never mentioned. I like the Japan version because the story and ending are intact.
lately i've been playing darkwing duck, abadox, and guerilla war. also, anyone here ever played code name: viper? it's a rip off of the rolling thunder style of games, but arguably is better (namco made rolling thunder while capcom made code name: viper). shatterhand is also pretty rad and i haven't ever seen anyone write about it.