It's easier to say which Ninty franchises I don't like or just don't get all their popularity: Mario Kart, Super Smash Bros., Pokemon.
The main three for me are 1) Zelda > 2) Metroid > 3) Mario (main platforming series, including Yoshi), followed by 4) Advance Wars, 5) Paper Mario, 6) Pikmin, 7) Mario & Luigi, 8) Fire Emblem. Notable mentions are 9) EarthBound, 10) Star Fox and 11) F-Zero.