GG Shinobi is an fantastic game. The second probably is too, but I barely played that one.
Micro machines was the best game to have if you had a friend, because you could both play simultaneously on a single console. Best multiplayer when holidaying outside with your best mate.
Ecco and Ecco 2 stand on their own compared to the Megadrive versions. Excellent 8bit conversion, and the new engine makes the game slightly easier.
I spent a lot of time on Lemmings. I remember being able to give skills to lemmings while paused, but every other version requires the game to be running. If true then this version has a massive advantage over the others and deserves to be played. Or thrown into a fire, depending how serious you are with your Lemmings gameplay.
I played Defenders of Oasis emulated on GBA during my commute a few years ago, it was a pretty cool JRPG. Quite linear and maybe short, but with an original theme and story.
The Shining Force Gaiden series have been fan-translated, and one was published in English. Fantastic, byte-sized version of their 16bit counterparts. No town to explore, everything is combat and pretty cool if you like the original games.
There were a lot of ports for the SEGA handheld that were great but ultimately the original 16bit was always objectively better. But back then they were the greatest things ever because they were your favourite games on a handheld. Stuff like Mortal Kombat 2, Super Off Road, Wonder Boy...
So many direct conversions of great Master System games, heck original Master System games could be played with an adapter. I tried not to put them in this list, some slipped through...
It's a super personal list, I didn't try to go for the overall top ten that you can find on the internet, instead give an opinion on the stuff I had and played.