Gunnerkrigg Court is a popular webcomic by Tom Siddell. It is written in the format of a graphic novel, and can in fact be purchased in book form, although it is difficult to find some volumes. Fortunately, the entire series can be found for free online.
The story is set in a magical boarding school. Not a school of magic, but a school with a strong sciences curriculum that happens to be surrounded by a magic wood that has boundary issues. The students learn subjects from robotics to applied mythology to Karmatron Dynamics, mostly through unofficial extracurricular activities.
Gunnerkrigg Court is not simply a school, however, but rather the ruins of a futuristic city, complete with monorails, artificial nature-park simulations, and robot sentries -- and endless streets of abandoned buildings. The students don't spend much time out and about the town, but even the school grounds are massive, and largely empty, enough that they never run out of places to explore and mysteries to solve. And most of the students are mysteries themselves, including the main character.
The story follows Antimony, a very bright girl who was sent off to school when her mother died, and who is, like the reader, somewhat confused by Gunnerkrigg Court. Her best friend Katarina "Kat" Donlan and her pet demon, Reynardine, find themselves at the center of a number of historical mysteries surrounding the decline of the Court and the ongoing conflict with the surrounding woods. Over the years, a number of new characters have appeared, including robots, pixies, forest spirits, various gods, teachers, and ghosts.
The webcomic has been running since 2005, and has thus far followed the main characters from year seven to sixth form, with no end in sight. Over this period the artwork has improved a good bit, but you should start at the beginning nonetheless. Their adventures are imaginative, complexly woven, and full of interesting characters and quirks.
Gunnerkrigg Court is the only graphic novel that I have really gotten into, so I cannot compare it to others of its genre. However, as a work of science fiction / fantasy it is engaging, well-written, and fairly epic in its extent and complexity. It also holds up well under multiple readings, and in fact requires multiple readings to pick up on all of the subtleties. It is perhaps just a little slippery in its construction of the story's world, as there are reoccurring references to the outside world as being our modern-day world, but at the same time the students are able to construct anti-gravity devices and robots with startling ease... of course, they are geniuses, so perhaps that's okay. There are times when the story slips into being just a bit too silly, but not in a bad way -- simply in a way that seems 'too unreal' compared to the majority of the story. Regardless, it is all very enjoyable, and addicting.
The comic can be found here. It updates about three times a week, although it should be read through from the start, so if you haven't read it yet you'll have a good bit of reading to do before the rate of output affects you.