It's hard to choose, as I had a lot of them. I'd go with the Fire Emblem, Metroid, Castlevania, Zelda, Kirby, Golden Sun, Pokémon and Drill Dozer games. And many great ports like all the Mario games (specially Mario 3), Zelda alttp, Shining Force and the Final Fantasy games.

For my top 5 Kirby & The Amazing Mirror, Zelda Minish Cap and Castlevania Aria of Sorrow, Mario & Luigi Superstar Saga and Fire Emblem Sacred Stones come to mind (in no particular order)

Edit: I forgot Mother 3! To be fair I only played it on emulators, so maybe that's why.