The ghastly line is pretty mean looking (totally not making a joke about them having mean look), though in a mischievous way.
Polywrath looks perpetually pissed off.
The GURRDURRRR line looks mostly retarded, but look like pissed off clowns.
Terrakion looks pretty menacing.
Thundorus, Landorus and Tornadus looks like they're always ready to f**k shit up.
Oh, and let's not forget freaking Giratina. That just looks like a bad ass mofo.
Though I think the winner in my book is Gyarados. But if you think about it, gyarados has a reason to look pissed as hell, with everyone ragging on magicarp.
Oh, and don't forget about Mewtwo. He might take the cake actually, since he's filled with nothing but hate and loathing.
Baa baa black sheep have you any booze? No sir, no sir, I'm a....sheep~