Homunculus, a really creepy underwater enemy. It just sits there until you approach it. Then, it starts thrashing wildly and trying to chase and kill you, while attached to this tube thing that gives it oxygen. That's not the worst part, though. If you don't kill the guy, he'll still follow you. Eventually, if you wander far enough from its spawn point, the tube will stretch too far and pop off the creature's back. The creature will be reduced to spending the last parts of its life thrashing and chasing you and turning purple as it slowly drowns.
Gergoth, the horrific boss of the Condemned Tower. It was apparently chained in captivity for thousands of years, and it looks like a half-rotten dinosaur, with exposed ribs and skin on its face that peels off when it's making an attack. You fight it, seeing its rotten flesh and dripping blood further emphasizing its cursed existence. Made even more disturbing when you read the text in the bestiary and find out it was once gentle, but was driven insane by years of imprisonment.
Puppet Master, the boss of the Demon Guest House. He's a giant creepy head with four arms sprouting from it. He has two attacks, the first being to spit dolls, which drain your MP, out of his creepy looking mouth. The other is to summon a puppet, which he slowly drags and places in one of the four iron maidens in his room. If Soma fails to destroy the puppet before it's put in the iron maiden, Puppet Master will use magic to make Soma switch places with it, dealing massive damage.
The final area of the game, the Abyss, contains loads of blatantly Satanic imagery and physics-bending area transitions featuring ram-horned skulls and giant knives with a single, bleeding eye entombed in the floors. And waiting at the end is Menace, a horrific fusion of all the souls Dmitri absorbs, with plenty of faces where there shouldn't be faces (there's one on his left knee, one inside his mouth, and a full head with an elongated neck embedded in his chest). Also, you're fighting him in an arena made entirely of human bodies, not to mention the cutscene before the fight, which ends with Dmitri screaming in agony as Menace bursts violently out of his back. In the first part of the Menace battle, he's trying to stab you with his ribs. Note, too, that Menace's eruption spills no blood; it's like Dmitri's been pre-exsanguinated.
The boss fight against Aguni. Aguni himself, while menacing in his own right, doesn't look particularly scary, but the shock of entering a mirror and being struck instantaneously by the first notes of Portal to Dark Bravery for the first time, coupled with a suddenly psychedelic battle background, can be quite unnerving.
