Shingetsutan Tsukihime (Supernatural/Seinen)- A lot of people pretend the Tsukihime anime never existed. The manga is nothing like the anime and is an awesome way to get a concentrated dose of Tsukihime's first two routes without the Nasu-writing.
Nowhere Boy (Seinen? Manhwa)- The amazing story of a whole bunch of cliches appointed by God to stop a faceless protagonist from ending the world in 100 days.
Uzumaki (Horror/Seinen)- Utterly unrelated to Naruto, this is my favorite Junji Ito work. It is about a town that is literally spiraling into madness.
I Am A Hero (Horror/Seinen)- Hideo Suzuki is a dead-end job mangaka with a gun license, a girlfriend who grows more distant from him by the day, and a ton of hallucinations. Or are they?
Petshop of Horrors (Horror/Josei?)- In Chinatown, there is a mysterious man who will give you the pet of your dreams... provided you follow some ground rules.
Akagami No Shirayukihime (Fantasy/Shoujo)- Wordy title, but it's like a loose retelling of Snow White in a relatively well-thought-out fantasy setting. Heroine is smart, art is cute, characters are likeable and relate-able.
Oresama Teacher (Shoujo)- Imagine if Great Teacher Onizuka and Beelzebub had a child.
Power!!/Girl Got Game (Shoujo)- It's like Hana Kimi
Shitsurakuen (Shoujo-Ai)- Vaguely like Utena, but the first 20-odd chapters will make you rage. Once you read past that you might find an intriguing, mind-screw story where everything you thought you knew about the world starts getting turned on its head.