Mother 3 because reasons that everyone knows.
Wario Land 4, amazing platformer with amazing levels topped with amazing music.
Kirby and the Amazing Mirror, the exploring and non-linearity of it which has the metroid exploration feel to it makes the game for me. Makes the game feel a lot bigger than what it actually is, which is pretty cool.
Metroid Fusion, the premise of the X is amazing, as these species have the ability to evolve and learn at insanely fast speeds. It's so fascinating and playing as Samus as she fights back from literally the brink of death and becoming a power house is so rewarding and thrilling.
Link's Awakening (DX), my favorite Zelda game for so many reason. I love the uniqueness and feel to it. Also has a very underrated soundtrack, especially the track Tal Tal Heights and Ballad of the Wind Fish.
Wario Land 3, not as good as WL4, but it's right up there. There's so much to do in this game. There's 25 well desigened levels with 4 treasure in each and it is not a chore to get each one. It's one of the only games i 100% and i have done it several times.
Pokemon G/S/C, my favorite region with my favorite set of Pokemon with my favorite starters with my favorite locations and favorite gym leaders with my favorite Champion. Also Jhoto is my favorite anime and I love so many episodes, well I guess not any of the gs ball episodes because fudge the gs ball.
Eh there's others but that should be good.