I really hope they keep getting darker as the Pokemon series continues on. >:D
My favorites would have to be Giratina and Yamask for reasons already mentioned. Yamask gave me the feels. I felt bad for using it. But I did anyway. Ironically it was one of the only surviving Pokemon in my last Nuzlocke run. >_>
Others I like are Parasect and Drifloon, because they're funny. xD. Most of the dex entries of Pokemon that you wouldn't expect to find creepy or disturbing at first (I know Parasect looks pretty freaky but I was ok with it at first. Just your regular old parasitic mushroom.) are hilarious to me simply because of the unexpectedness, and most likely the fact that Gamefreak never really intended for them to be so dark.
Hypno's made me LOL. Especially after Hypno's Lullaby. Pedo Pokemon; last thing I expected from a game geared towards little kids. When I saw this one I had a similar feeling to when I rewatch Spongebob while blindfolded. That whole 'WTF was I looking at as a kid' feel.
Oh also Cubone was another feels one. And freaky at the same time.
Originally Posted by Pokemon Stadium
Always wears the skull of its deceased mother on its head and never shows its face. It cries mournfully in the moonlight.
That one got me as a kid. Made me want to beat the holy crap out of Team Rocket too.