This one is just great fun. Suffers a bit from being just the first one (by which I mean I really want to get the rest now, to continue the story). The story of Agatha Heterodyne, a student at a crazy steampunk university, who gets drawn into a military takeover of the town. To complicate things, her secret (even to her) history begins to cause her trouble.
The stroy is pretty much beside the point, though. It's funny. The art is good (and also funny) and there's some great jokes in the dialog too. Also, I love the Jagermonsters, they rock.
Girl Genius 1 (Amazon)
You can read many of them at Girl Genius online, too.