My Little Alien: I knew there was something wrong with My Little Pony, I just didn't know it would come bursting through my chest cavity. This, and several more are from Mari Kasurinen, who has a Flickr page, a Deviant Art site and a website devoted to her custom toy creations.
My Little Edward Scissorhands: A misunderstood My Little Pony with razor-sharp blades for hooves. Marvelous! It even looks like Johnny Depp!
My Little Buckbeak: Nothing really horrifying about this custom My Little Pony, in fact the Buckbeak was a friendly to Harry Potter. I just loved the look.
My Little Boba Fett: If you have My Little Han Solo, you naturally have to have My Little Boba Fett. Now no more of this before George Lucas gets any ideas.
My Little Han Solo: Had carbonite freezing been available in my teen years, this is how all of my sisters Ponies would have ended up.
My Little Borg: If the Borg were to assimilate everything then it follows that they would assimilate My Little Pony as well. But it would be there undoing...
My Little Cthulhu: H.P. Lovecraft's embodiment of extreme horror, terror and evil, Cthulhu is a perfect candidate for a My Little Pony mod.
My Little Worf: Comes with his own bat'leth. I think Klingons would secretly love My Little Pony, just like they love prune juice — because they are both so terrible.
My Little Master Chief: The Chief isn't quite as imposing as a pony, but I'd happily stick a few plasma grenades on him, just to see what happens.
My Little Trojan Horse: Ah, the Classical Studies education pays off once more. How could the Trojan's resist bringing in something so cute? Which makes me wonder about Trojan condoms — oh sure, it's clever, there's something hidden inside! But when it gets out (and it does) it will slaughter you and burn everything you have to the ground. Hmm, guess that's why I'm not in advertising.
And for good measure, Robot Chicken's Apocalypse Ponies: Pestilence Pony, War Pony, Famine Pony, and Death Pony.