Any Miyazaki movie. I would say Soul Eater, but it's based in Death's academy... for all of three episodes, while the major plot that eventually comes out really only barely touches on the school... Air Gear's good, it's about genetically engineered humans who ride inline skates to get closer to god, no, seriously. It's basically Jet Set Radio with the insanity cranked up. While there are a few episodes based in the local school, they're only temporary, much of the story takes place in the alleys and underground. Hmm... what about FLCL? It's short, it's well animated, it's made by Gainax. Again, like, an episode or two in a school, but the plot is about extradimensional robots coming out of a kid's head...