Actually, it's pretty apparent ponies do not use a Dewey Decimal (or similar) system; Twilight is seen shelving a book about rocks (there's a memorably bad pun about the "The Official Handbook of the Marble Universe," which isn't even a pony pun) next to a book about something completely different because they were alphabetically next to each other.
Of course, this seems to be the case in the show; Pinkie Pie finds Twilight's Elements of Harmony book under E.
Actually, it's pretty apparent ponies do not use a Dewey Decimal (or similar) system; Twilight is seen shelving a book about rocks (there's a memorably bad pun about the "The Official Handbook of the Marble Universe," which isn't even a pony pun) next to a book about something completely different because they were alphabetically next to each other.
Of course, this seems to be the case in the show; Pinkie Pie finds Twilight's Elements of Harmony book under E.