I haven't read it in a while, but Highschool of The Dead is a great zombie/horror manga, though it isn't so much horror based as it is an action/adventure/dark comedy with horror undertones. The zombies are pretty much the only thing that makes it horror, and while it is pretty graphic at times, it isn't that 'scary'. Anyway, enough with semantics. My all-time favorite pure-horror manga is definitely the Corpse Party series. Very dark and graphic and certainly not for faint of heart. I love it though, there's something about elementary-aged ghosts and demons that is scary as hell. Actually, all kids are scary as hell, but these much more so than usual.
It's short, but I REALLY love Ibitsu. Perfect for fans of classic J-Horror stories.
Obviously, ANYTHING Junji Ito is good, but I like Uzumaki and The Enigma of Amigara Fault best.
And omg, all this Corpse Party love!! I hope you guys all play the games too. ;p They're even better! But yes, Corpse Party: Blood Covered is fantastic. I prefer it to the sort of fanservice-laden CP: Musume. The fanservice in Highschool of the Dead wasn't as intrusive as Musume's. :x