Gunnerkrigg Court, link to the archive so you can start at page one!
Picture Tim Burton with a dash of Harry Potter.
Young girl goes to a school where all sorts or strange things happen. While the students don't have magic (as far as I've seen, but I'm only up to June 2006 right now, just over a year into it), the whole story is full of it. Monsters, ghosts, dragons and dragon hunters are all real, just not in the way you'd expect.
It's really, really a unique story/world. "Magical" is the best word I have to sum it up.
One small warning: In general, the art is outstanding. I almost stopped reading on page one though, because the main character has no nose and thus reminded me of one of those Bratz dolls. Do not give up on it! It's really, really good!