Yeah late-gen Sunsoft games are very impressive both technically and gameplay-wise. Especially RotJ and Gimmick. They both used a special mapper chip only found in those two games. Another one is Ufouria/Hebereke.
Late Konami games are up there as well such as Crisis Force. Very impressive effects going on in that game. See for example the part around 2:45; vertical scrolling as well as horizontal scrolling side to side. Then the damn ground opens up, revealing fake-parallax scrolling canyon walls, while still maintaining the multi-directional scrolling that also becomes faster and faster, and with enemies flying up from the canyon using progressively larger sprites. That's just pure wizardry on the NES. Stage 3 at around 7:20 also has a canyon like that but with no horizontal scrolling. But they make up for it by putting more parallax scrolling walls in the canyon instead.
Natsume games are also up there, like Shatterhand.
I also want to mention Punch Out!! for the detailed facial animations and large sprites. And Super Mario Bros 3 as well but that's pretty obvious.
Late Konami games are up there as well such as Crisis Force. Very impressive effects going on in that game. See for example the part around 2:45; vertical scrolling as well as horizontal scrolling side to side. Then the damn ground opens up, revealing fake-parallax scrolling canyon walls, while still maintaining the multi-directional scrolling that also becomes faster and faster, and with enemies flying up from the canyon using progressively larger sprites. That's just pure wizardry on the NES. Stage 3 at around 7:20 also has a canyon like that but with no horizontal scrolling. But they make up for it by putting more parallax scrolling walls in the canyon instead.
Natsume games are also up there, like Shatterhand.
I also want to mention Punch Out!! for the detailed facial animations and large sprites. And Super Mario Bros 3 as well but that's pretty obvious.