While the story hasn't be declared yet, Discorded Celestia: Not Loved gave Discord the middle name Apophis and last name Typhon. "Different From Everypony Else" had this made his official full name. Also both a bit of Genius Bonus and Nightmare Fuel to fans of mythology who know just what those names mean.
This piece of fanart (a sequel to a certain scene in Dark World) was eventually inserted into the fic.
Alexwarlorn noted that despite describing Pandora with a fox's tail, fanart kept showing her with a lion's tail instead. Eventually, he had Discord comment that Pandora went through a phase where she replaced her lion tail with a fox's for a while before going back.
The Nameless Passenger in Dark World is eventually revealed to be an evolution of Nightmare Purgatory from the "Fading Futures" Recursive Fanfiction.
Ascended Meme: Cutie Mark Failure Insanity Syndrome gets a shout out in Shining Armor's 10th chapter.
Creative Differences: Seems to be a genuine case between Alexwarlorn and LZ0291 given their comments, as a number of their arguments seem centered around the directions the fanfic goes in. While neither sides have parted ways, LZ has come close on a number of occasions and the two fight from time to time in the comments.
Creator Breakdown: Alexwarlorn has had several over the course of the story, though thankfully he's managed to recover each time and it hasn't effected the story much.
LZ0291, the writer of the Shining Armor arc, suffered one, feeling that no one cared about his arc and was seriously considering quitting the project. Fortunately, the fans let him know that they did care, and he recovered. It was later revealed this was in part due to clinical depression.
Godzillawolf has also had minor one due to Real Life events (including the death of a family member) putting tremendous stress on him combined with various Troubled Production related issues. He managed to recover, thankfully, and the story wasn't effected.
I Knew It: Despite refusing to watch season 3 till the fic is done, the author actually managed to predict plot points in about half the episodes of it. See Hilarious in Hindsight in the YMMV page for details.
Promoted Fanboy: Kendell2 started out as simply a fan, then became a beta reader before actually getting to write some scenes a finally even threechapters, including a Shining Armor arc chapter written to supplied notes, and co-writing the chapters from 14 onwards. He refers to himself as this trope in the description. He also wrote the original lyrics for the original Reharmonized audio adaptation's theme song, though they were altered somewhat for the final version.
Alexwarlorn wasn't originally supposed to write any of the 7 Dreams/Nightmares chapters, but ultimately had to write Bright Eyes' story due to losing contact with the original writer.
Chapter 36 of Dark World originally had scenes of Amicita restoring Neo Stream to existence and healing/redeeming the Emperor of Man. However, complaints from Neo Stream's owner in the former case and pressure from critics in the latter case forced Alexwarlorn to remove both scenes.