The most creepiest Pokémon to me is hypno because of hypno's lullaby search it and it will creep you out.

I'd say that Duskull is, since one of it's pokedex entries states that it chases after prey until dawn, it spirits bad kids away and  it loves the crying of children.

The Pokèmon that scared me the most when I was a child was Cubones mother when you encounter her in Pokèmon Tower in Lavender Town. Just the combination of the environment and the creepy music that starts playing makes her really scary when you first see her, especially if you don't have the Silph Scope. Despite her being a ghost I always wanted to catch her, I just thought I could save her and it would somehow make her happy. It just seemed cruel that you had to pretty much destroy a ghost that was just defending itself and more than likely it's child.

As a legit Pokemon it would be Gengar, it literally has the power to posses you and kill you. You also can't see it coming because it's pretty much a shadow and you can only tell if it's coming if it shows itself to you or if you hear it laughing.

Here's a cool article I found that lists 10 really disturbing Pokemon and is definitely worth the read.
http://www.comicsalliance.com/2011/03/15/weirdest-pokemon-black-white/

It is obviously Weezing because it has two heads (I think and if not it has more) and its always just feels wierd to me (but not because of the two heads)!