Hmmmm... its either going to be something from Metroid or Zelda...
Ugh, this is hard.
I'll say the Wind Waker. Its the only Zelda game that can ferret some genuine emotion out of me, the sense of scale is still there with the Great Ocean even after playing Twilight Princess. And while I find Twilight Princess both beautiful in terms of art style and narrative, Twilight Princess is very much a melancholy game with characters who are emotionally distant (and quite rightly so, given the state of things) But Wind Waker can bring me a myriad of feelings as soon as I load it up, whereas with TP i kind of have to look at the whole picture.
In Wind Waker i see Nintendo's heart, this is the kind of game they love to make, they like to make gamers happy, they like to make them smile and give them true world. Wind Waker is pretty much the only recent Zelda which didn't concern itself with out-doing Ocarina of Time too, which makes it even more special. It really shows that Nintendo put their hearts into this one and were eager to give us it as soon as the technology was ready, they stood by the early trailers and screenshots because they knew what they were doing, they didn't cave into the backlash and now look at it, WW is possibly the crux of Zelda as far as graphics go now with the cel-shading being used numerous times since with a growing number of fans wanting each Zelda to follow the trend.
Everything in the Wind Waker was loved and it shows which is something that i've never really felt in a video game before. The only game that comes close is the seemingly natural and meant to be seen beauty of some of Metroid Prime's locations, but where I say 'some locations' for Metroid Prime, my love for Wind Waker encompasses all locations and the entire game. So thats my choice, Wind Waker is my favourite game of all time.. shocking i know i thought i'dve said something different too...