Sonic's shoes and Earthworm Jim's gun appear in the corner off to the side at the end of Donkey Kong Country 2, when Diddy and Dixie on that glam-ified platform to compare with Mario and Yoshi.
And if you didn't get enough DK coins, Link will be on the third place pedestal.
In Donkey Kong Country 3, the Bear right next to the first Save Cave will occasionally describe a boy in green walking out of his store grumbling that the Bear's store had the wrong sea shells. It's a reference to the Secret Seashells in Zelda: Link's Awakening.
In the original Final Fantasy, in the Elf town, there's a grave marker that reads "Here lies Link."
In Zelda: Twilight Princess, you might notice that the guy who runs the minigame tent in Castle Town is dressed up as Tingle.
When the Postman delivers something to you, he hums the infamous tune of solving a puzzle that has been a part of every Zelda game since the beginning.
In Viewtiful Joe, when he's talking with Hulk Davidson before fighting him, Davidson asks "Who do you think you are, some of 'Mega Man'?"
In the original Gamecube version, Joe will whistle bits of the Super Mario theme when holding a bomb. Also, a Nintendo Gamecube will appear among the flotsam and jetsam spewing out of Gran Bruce's mouth in 2,000,000 Leagues Under the Sea.
Those are some of my favorites. I'll post some more when I can think of them.
