Illusion of Gaia (SNES) - Lots of people play Soul Blazer or Terranigma but forget about the great game in between them.
The early Harvest Moons - If you're a HM or Stardew Valley or whatever-other-farming-sim fan: Don't neglect the earlier games. They had a lot of charm without packing in 20 million things to do.
Zelda: The Minish Cap - We all have a top 5 Zelda games list in our heads, and any of us who doesn't have Minish Cap in it that list is incorrect.
The first Harvest Moon I ever played, was the game boy one. I was getting into emulating, and downloaded it on a whim. There wasn't even a town you could explore, only a map with various stores and the like to select. I literally stayed up all night playing it.