Right now, Borderlands 2's the Dark Souls and Minecraft Easter Eggs stand as my two favorite of all time, simply for sheer commitment to detail. BL2 really went all out with their easter eggs.
But I do so enjoy the ones I come across by accident, like the completely out of place paper plane you can find in Ikana Castle in Majora's Mask on top of a stone pillar.
It just chills there. Not used for anything. I love little things like that that are just there because. And small ones such as noticing the Mario mask on the back of the Mask Salesman's pack. It even shows up in the official art of the character.
Wind Waker has some masks from MM hidden in the back of the Picto Gallery behind the counter.
I mean there are a ton of references in the Zelda games, way too many to count. It's just that these ones are easy to find on your own, but aren't presented right to you. Unlike the Dark Souls one in BL2, which there was no way I'd have found had I not seen it first online.