^This. Also, when I pet Gengar, the hand becomes ghostly!
Yeah the Gastly / Haunter / Gengar line you don't actually touch at all. Your hand goes through them. Makes sense, considering they're ghost pokemon that, at least for Gastly, are made of poisonous gas. They seem to enjoy having you inside them, though...
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I think petting the cloud on Drifloon's head has the same effect as petting Gastly/Haunter/Gengar, and you get a different sound petting it than you would from anywhere else on its body.
Like mentioned before, Gulpin gulping down food in one bite.
I've seen special sleeping animations for Lucario and female Meowstic. Meowstic lies flat on the ground on its stomach, and slowly gets up when you wake it up. Lucario is sitting while it sleeps, and looks up at you when you wake it up.
When you pet the fluffy white fur around Yveltal's neck, it closes its eyes and opens its mouth as if to say "Yeah, that's the spot!" It's cute and kind of funny coming from the personification (Pokemonification?) of death.
I like how if you touch the screen beside most Pokemon and drag it around, they'll open their mouths and tilt their heads to follow your hand.