So after my post about MS Paint Adventures, I felt kinda guilty for leaving out the other webcomic that I read*: Gunnerkrigg Court. (Google it!) It's a bit more seriousface than MSPA, but that by no means indicates it's any less awesome.
Gunnerkrigg Court is an institution that harnesses the pinnacle of man's technology, while dabbing a bit in the realm of magic. (Though, don't let this scare you into thinking you need to be tech-savvy to understand it.) It hides itself from the entire world, despite its vast size, and manages to cloak itself as... a school.
So, don't be scared that the main character is a young girl who is just starting her education there! (And no, this is nothing like Harry Potter. :P)
*Okay, so I also sporadically read lots of Dinosaur comics