I've been reading a lot of Junji Ito stuff and highly recommend him. A lot of his stories have a similar setting or focus, but his stories range from Lovecraftian to Body Horror to psychological to just plain creepy. They are almost all supernatural, which really keeps you guessing. He is excellent at using a tired concept like a haunted house or a ghost or a monster and twisting it to where you have no idea where the story will go next. While he is known in the west mostly for longer stories like Uzumaki, Tomie, and Gyo, his short stories are really his masterpieces. In 30ish pages he can burn an image or idea into your brain forever. I have to admire his unique concept in all his stories. He has a ton of stories, and obviously some are better than others, but I was always impressed by the potential and initial idea. Here are a few recommendations:
Longer (several volumes):
Uzumaki: People become obsessed with spirals in a small town. Ito really impresses by taking a simple and non-scary thing and using it in many amazing ways.
Gyo: A horrible stench and fish with robot legs cause panic. Probably one of the more bizarre concepts, but I really enjoyed it. I think there's going to be an anime too.
Tomie: An immortal girl with strange powers ensnares all who come in contact with her. One of his earlier and more famous works.
Medium (about a hundredish pages or only a few chapters):
Frankenstein: An adaptation of the original story.
Hellstar Remina: A planet-sized monstrosity from another dimension heads for Earth. The Lovecraft influence is strong here.
Black Paradox: Four people plan to commit suicide together, only for strange events to postpone their death.
Souichi's Diary of Delights/Diary of Curses: More of a black comedy instead of straight up horror (although the Haunted House chapter could definitely be a standalone story, but the following chapter puts an amusing ending on it). About 12ish chapters, the story follows Souichi, a mischievous 11 year old who is obsessed with voodoo and curses. His powers are legitimate, but he always gets his comeuppances, largely thanks to his family.
Mimi's Ghost Stories: Four chapters that follow Mimi and her friends. A girl gets into all sorts of supernatural mishaps. The Seashore and The Woman Next Door are highlights.
Short stories (he probably has hundreds, but I'll list some I like):
The Enigma of Amigara Fault: It's been posted here before so I think most people know it. Strange human shaped holes in mountains appear after a massive earthquake, which cause people to flock to the site.
Anything but a Ghost: A man finds a woman covered in blood when driving. After rescuing her, he learns that there may be more to her innocent demeanor.
The Window Next Door: A family moves into a new house, but one member is constantly harassed by the neighbor across the street. Such a simple concept, but damn his art makes it so creepy.
The Groaning Drain: A family obsessed with cleanliness are tormented by a drain that won't come clean.
The Town Without Streets: Really it's three stories in one, but a girl who is creeped out by her family goes to visit her aunt in a strange town where no one has privacy.
House of Puppets: Your typically "puppets are scary" story, but with those classic Ito twists and creepy art.
Splatter Film: A group of friends become addicted to a mysterious honey. However, there may be side effects.
Library of Illusions: A man becomes obsessed with memorizing every book in his massive library.
Army of One: Strange murders where people are sewn together may have some connection to large group gatherings.
The Conversation Room: After being admitted to the hospital after a car wreck, the protagonist is disturbed by the other patients.
The Long Dream: INCEPTION uh I mean a man's dreams become increasingly long each night, where each dream can last lifetimes.
Blood Bubble Bushes: A couple find themselves in a town where people are obsessed with drinking blood.
Blood Sickness of White Sand Village: A doctor investigates a town where people lose a rapid amount of blood very quickly.
In the Soil: At a junior high graduation anniversary event, two former classmates discuss a student that nobody liked.
There are of course, many more. He's put out a massive body of work in his career. Now for dat art:
I can't post the really good stuff due to spoilers/NSFWness.