Metroid became a core franchise thanks to its huge resurgances on the Gamecube.
On every Nintendo system I think you can place titles from these franchises as the stand-out games that people think of when they think of that generation.
For me:
NES: Super Mario Bros (1 or 3?)
SNES: Legend of Zelda: A Link to the Past
N64: Super Mario 64 / Ocarina of Time
Gamecube: Metroid Prime
Wii: Super Mario Galaxy