Twilight in wolf form. He's a literal wolf. Growling and barking dogs are scary even to dog owners, not to mention a giant wolf with ominous markings and intelligent eyes. Twilight on his own can look kind of intimidating, I guess, but he's also quite short, which ruins the effect on most people.

Mask with the Fierce Deity mask. Or the Goron mask, giant's mask, one the masks meant to help him fit in with the undead, the one that literally blows up, etc.

Wild with full access to his spookiest clothes + swimming up through the floor + summoning machines of terror

Sky when he's really, really mad.

Cap (with his magic rod especially, but the gauntlets and other setups are pretty scary)

Vet when using one of his medallions

Mouse when throwing fire and lightning around

Anyone else with a fire rod

Aspect, since Hylians aren't familiar with someone who looks like him. They don't know how to read his expressions, and he has claws.

I'd include Gen, but he is mostly just stern-looking when he chooses to be. He also has droopy eyes that remove some of the intimidation factor. He's an honorable mention, though.

But all of these are circumstantial, and almost all rely on items. And Sky can't make that expression on command. It's really rare to see.