Well, if we're only going off internally-developed Nintendo games with no outside help, I'll vote for OOT. Those of you that were there when it dropped back in the day and played it all the way through for the first time with the lights off, alone... you know what I'm talking about. It was as close to experiencing The Neverending Story as you could get.

Paper Mario TTYD, one of the funniest game I've played.

Majora's Mask & Mother 3

For me personally, I'd give it to the original Xenoblade Chronicles.

It does such a great job of gradually revealing tantalizing bits and pieces of the narrative picture, then pulling back to reveal that what we thought we knew is only a smaller part of an even bigger picture. This steady rhythm is maintained really well over its long runtime, backed up by a likeable cast.