I agree with hawkflame, especially after chapter 104. Father takes freaky to a all new level.

Quite. Why does he have such an aversion to having the right number of eyes oh gosh

Envy's freakish form in Ep. 28. 'Nuff said.

Terminarcher. That was a complete departure from science. Half his head was blown off, for God's sake!

Grusome, but would you like to see a beast with several vomit-green, decrepid, grusome souls forming it's skin?

Oh you mean Envy's beast-with-six-legs form? He not all that freaky in that form. To me he just looks like a six-legged animal with some godawful plastic surgery.
But, if I saw that thing in real life I'd be just a little freaked out. Just a little.

I think Pride posesed Al was creepy! I dunno, I saw it in the manga and it freaked me out,
especially with the eyes looking narrowed and scary. It wasn't so bad in the anime, but
still it gives me goosebumps.

Personally, Anime1Envy had his scare highlight as well. Sure, he didn't have a monstrous-looking form like his manga counterpart, but the fact is he embodies the dark side of Edward Elric. He is what the hero could have been if he had no Al or Winry, if he allowed his father-issues to rot his soul. To look at that evil, and see something of yourself in that evil (beyond the shape-shifting); now, that's pretty freaky!

It has to be Father for me from the manga... at first his form is stable but in the recent chapters it's gone from bad to weird to WTF! Even the unamused bishie form is freaking me out now... O_o He's not even human, and considering he's the source of all the homunculi, all their ugly is part of him too...

I wouldn't go as far as to say they're scary, but Kimblee, Selim, & manga!Father are the first ones that spring to mind for "freakiest" characters.

^ I've got to agree with that. Selim's shadowing of Riza *shivers*

And as much as I love her, Sloth from the first anime. Spreading her arms as if to hug, liquefying them, and saying "Why didn't you transmutate me correctly" (paraphrased) is seriously not a comforting sight. Then there's her power, transforming into water and appearing to not even have feet to walk with (her dress touches the floor so you couldn't see them, but notice how she seems to just swish around rather than walk?) is pretty messed up. And she's almost always so eerily calm...even with all the inner turmoil. 0.0
Yeah, I agree with above posters, Terminarcher is a disturbing sight. o_o
Shou Tucker too...
And the Gold Toothed Doctor!

The freakiest of them all, to me, is Manga!Father. IMO he is certified freaky.
Although, when I saw the "failed transmutation" first time in FMA-1, that spooked me quite a bit.

Manga!Father I think is the creepiest, but the character that really scares me the most is Truth.
Just the fact that he's everything, he's always there, he's inevitable. You can't escape from the Truth.
And I suppose the scariest part is that the same goes in our world too. The truth might not be a shapeless blob-man who takes people's limbs and little siblings, but it's still there and there's no escaping it.