Special Topics in Calamity Physics by Marisha Pessl is quirky and wonderful. Shirley Jackson's Hangsaman focuses on a damaged young woman off at college.
If you like suspense, several of Carol Goodman's books are set in schools in upstate New York; I've read some of the standalones, including Arcadia Falls, River Road, and The Widow's House, all of which I enjoyed.
More in the suspense genre: Michele Campbell's It's Always the Husband is set at a university, but I didn't like it. I did enjoy Joanna Goodman's The Finishing School. The Most Dangerous Place on Earth by Lindsey Lee Johnson is set in high school; it was pretty good. I liked Kate White's The Sixes, about a secret campus society.
For YA suspense, you might consider several of Lois Duncan's books--Daughters of Eve, Killing Mr. Griffin, Down a Dark Hall, Gallows Hill, etc.
For humor, I recommend Max Shulman's hilarious books, especially The Many Loves of Dobie Gillis, and Julie Berry's The Scandalous Sisterhood of Prickwillow Place.
A few more: To Sir, With Love by E. R. Braithwaite, Up the Down Staircase by Bel Kaufman, and The Blackboard Jungle by Evan Hunter.
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