And That's How Equestria Was Made

Alpha Bitch: As in the show, Diamond Tiara.
Aluminum Christmas Trees: This comic features a pony Batman. Sounds ridiculous, but when you consider The Mysterious Mare Do Well...
Bread Eggs Milk Squick: The multiple choice answers to Twilight's question in this strip:

a) Ask for a third opinion.

b) Respect each others tastes.

c) Find new friends.

d) Kill each other.

e) Start raving with classical music.

Cloudcuckooland: Referenced in the title of this strip.
Crack Fic: Here.
The Ditz: Derpy.
Everyone Is Satan in Hell: This strip has Derpy Hooves' brief replacement applying this to the show. Her reasons start out reasonable, but get more and more ridiculous. It was just an Acid Reflux Nightmare Derpy had from eating a Zap Apple, though
Fur Is Clothing: Parodied.
Hypocritical Humor: Discord here.
Mistaken Identity: Spike mistakes the Elements of Harmony sea serpent for Rarity.
Motivation On a Stick: Here.
Pick a Card: Trixie does this here.
Prince and Pauper: Here.
Public Service Announcement: Regarding dental hygiene
Real Life Writes the Plot: The strips are usually inspired by recent episodes.
The Scrappy: Invoked with Trixie.
Shout Out:
- To The Powerpuff Girls in the first strip. (May also be a Mythology Gag, as Lauren Faust also worked on that show)
- The sound effect here is RAINBOW'D!
- A possible one to The Fairly Odd Parents: Channel Chasers in this strip.