Hey Everypony,
This is the (to date) Chronology of my My Little Mages stories. Please Note that dracone's My Little Mages: After Effects is part of this, the exact order is still being worked out between us, but this should help everypony get an idea of the order

My Little Mages: The Revenge of Nightmare Moon
My Little Mages: Erisomachy
My Little Mages: The Cutie Mage Crusader Dream Trilogy
My Little Mages: The Royal Wedding
My Little Mages: The Grand Gala
My Little Mages: The Phantasm of Philanthropy
My Little Mages: The Siege of Krystalopolies
My Little Mages: Enchanted Enigma Elixir
My Little Mages: The Lost Student
In the Chambers with Twilight; A My Little Mages Supplement
My Little Mages: Weight of the Crown
My Little Mages: The Rainbow Keys
My Little Mages: Kingdom of Friendship
My Little Mages: The Sirens' Song
My Little Mages: The New World Map
My Little Mages: Goddess of Midnight , My Little Mages: The Remarking of Time
My Little Mages: The Anointing / My Little Mages: Anima Gaea Semperlibera / My Little Mages: The Pillars of Virtue/
Conversation on a Train: A My Little Mages Supplement
My Little Mages: An Apprentice’s Holiday
My Little Mages: The Mirror of Shadow Bolt
My Little Mages: Seraphic Guidance
My Little Mages: Omitted Tie
My Little Mages: The Play of Shadows
My Little Mages: Amicitiae Tempestate
My Little Mages: Academia Amina
My Little Mages: Academia Ardens
My Little Mages: Harmonic Turbulence
My Little Mages: Duration Disuption
My Little Mages: Onset of Resolution
My Little Mages: The Perfect Present in Perpetuum
My Little Mages: End of the Rainbow
My Little Mages: Denouement of Resolution
My Little Mages: The Shadows' Revenge
My Little Mages: Subrosa Admission
My Little Mages: The Ultimate Obstacle

Additional Works in the series:
My Little Mages: After Effects, The Great And Powerful Amendments
My Little Mages: The Roques' Entries

(As more stories are published they will be added)