This is one of those topics for the day where part of me wants to say "Do you really have to ask?" *winks*
But I'll bite - I have a few books I really enjoyed set in schools, magical and otherwise.
I'll name six off the top of my head. The first one probably shouldn't surprise anyone - I loved the Harry Potter series (even if I haven't read the last book because I was spoiled silly when it first came out *cough*). J.K. Rowling is love, enough said.
Kara Taylor's "Prep School Confidential" seriously impressed me as a YA work, and it remains among my all time favorite books (and series!). I love the overarching mystery, the feisty heroine, and just how hilarious it was between the guesswork I had through the narrative's events.
Anna and the French Kiss by Stephanie Perkins still remains one of my favorite narratives written not just in a school, but a school set overseas. I felt like it worked the environmental details and the characterizations so well. And it was full of good humor and sweet moments despite some caveats.
Hex Hall by Rachel Hawkins and Shadow Kiss by Richelle Mead both are choices I would make for paranormal school stories that had a combination of humor and harrowing events, with a strong cast of characters.
Lastly, a favorite of mine since I was in high school, "The Lake of Dead Languages" by Carol Goodman was a gothic school story I really enjoyed not only for its attention to Latin, but the mystery surrounding the old boarding school and its student body. I think that was the book that first introduced me to Carol Goodman.
I think that's all for today's entry. Looking forward to tomorrow's prompt!