Every book is a reference. Some of them are cheekier than others. How many can you name? Both canon and some sneaky fanfic references included. Updated quality. Zoom in to read. Thumbnail quality is bad.

Sunset's Library, from left to right, top to bottom:

Magical Field Theory
Ancient Equestrian History
On the Shoulders of Giants
Magic Monopoles
Flanksy
Sunset Sutra
How to Be Assertive - Iron Will
The Celestia Delusion
The Equine Predicament
Mathematical Methods for Magical Ponies
Leyline Theory
Magical Matrices
Calculus - Stewart
Spacetime and Geometry - Sean Carroll
Magic for Dummies
Starswirl the Bearded - an Autobiography
The Monster Book of Monsters by Edwardus Lima
Quantum Field Theory
Griffiths E&M
Magical Thermodynamics
Celestial Mechanics by Princess Celestia
Sunset's Journal
Element's of Harmony - a Reference Guide
The Journal of the Two Sisters
Daring Do: The Complete Works
Encyclopedia Equestria
Pennyroyal Academy - M.A. Larson
Journal of Friendship
Slime & Punishment
Anon in Equestria (AIE) - A Compendium
Transfiguration
Enchanting
Thaumaturgy
Abjuration
Conjuration
Black Magic
TIME (Magazine)
My System - Aaron Nimzovich
Cozy Glow (Bobby Fischer) - My 60 Memorable Games
The Amateur's Mind - Jeremy Silman
My Great Predecessors - Kasparov
Think Like a Grandmaster
The Star Swirl Decimal System
Star Swirl's Journal
Alabaster Comethoof's Journal
Anthropology
Bon-Bon (recipes)
How to Win Friends and Influence Ponies - Twilight Sparkle
Music Theory For DJs
Starlight's Manifesto
Necronomicon
How to Succeed in Magic and Die Anyway