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. I had a lot more ideas for books but I could only fit so many :(.

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

Magical Field Theory
Ancient Equestrian History
On the Shoulders of Giants — Stephen Hawking
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 (A.I.E.) — 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 — Alexander Kotov
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 — H.P. Lovecraft
How to Succeed in Magic and Die Anyway