I mean I guess I can't forget to mention Mario Sunshine, Pikmin, Luigi's Mansion, Animal Crossing, Super Smash Brothers, Kirby and Pokemon. Surely those hold a special place in peoples hearts.
However, the ones I feel like I missed was Skies of Arcadia, Phantasy Star Online, Alien Hominid, F-Zero GX, Bonk's Adventure Remake, Metroid Prime series, Zelda: Ocarina of Time Master Quest (since I never even played the original Zelda Ocarina of Time), Zelda: Twilight Princess, Zelda: Windwaker (I've grown to really like the Cel Shading style since playing Jet Set Future a long time ago and seeing Jet Grind Radio make a return of sorts), and Megaman Battle Network.