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Shiny Lapras is the same color as Tessie, both being based off the Lochness Monster.
The maids in Black / White are dressed exactly like Li'l Miss Marshmallow from Mother 3, right down the the color pallet and look.
The Barrier Trio have an odd resemblance to the Trio from the R/S/E series, though this is most likely coincidence.
Muk is shiny while green, much like Master Belch, this also is probably coincidence.
Titanic Ant strikes a similar look to Durant, both are metallic ants.
The new Tree Pokemon could also be a reference, but Tree monsters are common among RPGs, especially JRPGS. So, I am assuming they were probably deciding to finally introduce a Pokemon as a JRPG staple. Unless it knows Aftermath or explosion, then it's blatantly referencing all the tree enemies from the MOTHER series.
I know there's more, but I can't think of them all. OP's picture is also one I have noticed.