One of my more recent favorites is how Link will sometimes swing his sword triumphantly before putting it away in The Legend of Zelda: Twilight Princess, but I also
love Mario's sleepy mumblings in Super Mario 64, Dixie Kong sipping from a juice box in Donkey Kong Country 3 as an idle animation, and how Banjo - Tooie allows players to
revisit some
areas of Banjo - Kazooie that were destroyed or otherwise impacted in the previous adventure (Spiral Mountain and the entry of Gruntilda's realm come to mind).