Easily the creepiest, most effective horror comic I've read, and probably my favorite manga to date, has been Uzumaki, a three-volume Lovecraftian horror tale by Junji Ito. So his follow-up series, Gyo, was a must-buy, and though I worried that my higher expectations might result in a bit of a letdown, in fact I was quite happy with the first volume. Gyo isn't completely unlike Uzumaki, featuring horror that revolves around infection and mutation of the human body to some extent, but it is also a very different sort of horror, featuring very physical and explainable monsters instead of just a creeping horror. Gyo also has the same ability to make the ridiculous seem scary and horrifying; certainly I wouldn't have imagined that swarms of fish walking on legs could be so terrifying, but Ito pulls that, and several other strange ideas and visuals, off.
While Uzumaki was structured as a series of short stories, each one introducing different aspects of a single horror, Gyo introduces a single horror in the form of a small event and then builds upon it, until eventually what was one creepy occurrence has become an infestation and epidemic. His focus is on a young couple, the annoying and demanding Kaori and the put-upon Tadashi, and while neither of them are particularly likable characters, they are normal enough to make the outlandish events seem more horrifying. Interestingly enough, it's the addition of a smarter character, one able to step back from the events and examine them from a scientific point-of-view, that actually deepens the creep factor, because that character's emotional detachment from his own rather immense personal experience with the horror is a bit creepy in and of itself.
Ito is clearly a master of pacing and timing, which is so important when writing a horror manga. He keeps the monster in shadow, revealing it slowly, and provides a few fakeouts so that we don't always know when the monster is going to appear. He conveys the unearthly nature of the creatures with his artwork, and conveys their speed and ability to appear from nowhere or become a terrifying mass very well. Fish and other creatures of the sea have a strange, alien appearance that can be frightening anyway, and the addition of organic walking apparatus on top of that alien appearance is very effective.
Another thing that makes Gyo work is Ito's imagination, which often manifests in the ability to make the weird and sometimes downright ludicrous scary. The notion of a "landshark" is something that inspires laughter, but when you see a Great White Shark moving around on land, driven by the same ferocious predatory instincts but without the limitations of being stuck in the water... well, it makes the shark in Jaws look like a big wuss by comparison. Similarly, the idea of a whale rising out of the water on legs might seem more silly than dangerous, but when the whole of the city is overrun by scrambling, creepy fish on legs, an enormous fish with the same ability to move is truly disturbing.
Leaving aside the fears that come from the creatures rising from the sea, Ito also injects a bit of horror in the form of that 21st century fear, the fear of plague and infection. The notion of a corpse-like smell rising from the creatures makes them not only more noxious but more frightening, and it's all too easy to imagine being immersed in a choking, nasty smell that you can't get free of. The notion that the smell could also be a dangerous, infectious agent, capable of mutating a beautiful girl like Kaori into a monstrous creature, makes it even worse, and like the notion of a shark on legs or a village terrorized by a spiral pattern, it gives the sense of an unescapable menace, which makes the whole thing all the scarier.