Well, I grew up with the Nintendo64, falling in love with so many titles on that fabulous console. It set the stage for every 3D platform after all it, breeding all sorts of puzzles, both simplistic and challenging. Two of the best Zelda games derived from it also, and while I only spent my childhood with one (Majora's Mask) they both have come to be on top of my list. They've equally produced memories that will stick with me till my whiskers revert to gray.
Of course I'm now playing Skyward Sword, and its controls are "connecting" me closer to the story and setting more than standard controllers could. It's sure to stake its place amongst my favorites as well, but not overcome them, because I love each (including Twilight Princess) the same, but for different reasons.