As for pokemon, I dunno. I wouldn't say that in the world of pokemon, they would make direct references to Nintendo characters; maybe small hints of say, instead of Link, just... a boy in green. But, it'd be kind of weird if they started doing that, imo. It'd be an Easter Egg at best, but other than that? Not very likely.
I think that'd be interesting in a way, especially if they kept the description sort of vague yet noticeable by someone who's played other franchises. With X and Y using cel-shaded graphics and how the protagonist is always silent, how funny would it be if a coastal town(assuming the games have one) local referenced Toon Link from Wind Waker by saying something like 'your silence reminds me of a mysterious (elf-looking) blonde guy in green who sailed through here x months/years ago'.
Sure it would kind of ruin the uniqueness of the Pokemon world but I think it'd be some good fun to leave in easter eggs like that every so often. I just would hope obsessed people wouldn't force an explanation for such a thing.