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