My top 3:
3. Treeehouse of Horror V - The Shinning, Time & Punishment, Nightmare Cafeteria
This is my favorite Treehouse. "No TV and no beer make Homer...something something....."
2. 22 Short Films about Springfield
For the many reasons mentioned, it's just a sublime slice of side-characters and really defines so many of them.
1. Cape Feare
Perfection. Period.
Honorable mentions go to Trilogy of Error, Seperate Vocations, Homer at the Bat, Lost our Lisa, The Book Job, Itchy & Scratchy Land - all fantastic!