The Secret History by Donna Tartt
Each autumn, I reread this book to get into the cozy mood. For those few who haven't heard, it follows a debauched group of friends at a college in Vermont and is completely flawless.
Still Life by Louise Penny
A warm novel set in a small town that pairs crime solving with descriptions of French-Canadian comfort food.
The Hotel New Hampshire by John Irving
The story of a family of hoteliers in New Hampshire.
The Harry Potter series by J.K. Rowling
An obvious choice for their combination of magic, academia, and pumpkin based treats.
The Starboard Sea by Amber Dermont
Any book set on a college campus or prep school makes for excellent fall reading. This one is about a student at a prep school in the late 1980s, sailing, and emotion.
The Halloween Tree by Ray Bradbury
A classic short novel with all of the essential elements of Halloween---druids, the dark ages, gargoyles, and catacombs.
The Catcher in the Rye by J.D. Salinger
Another prep school pick, perhaps the most essential of them all, although the mostly New York setting makes it even more fall-worthy.
The Tenant of Wildfell Hall by Anne Bronte
Dilapidated mansions and the English countryside---all that needs to be said.