Moonstuck itself has an affectionate parody in the form of Dark Moonstuck. It was made to follow the life of the original Woona who was jettisoned into space at the start of Moonstuck on this page and is drawn by a friend of Egophiliac in a beautiful style. The adventures are semi-canon.
Dark Woona also counts, considering she successfully steals a relic guarded by rocs and holds her own against the Changeling Regent. There's also her constant defeats of Woona in direct combat, despite Woona herself hardly being bereft of magical power. Of course, since Dark Woona is actually a puppet controlled by Discord, this isn't surprising.
Very early on in the series, Woona learned "underwater basket weaving" as a quick joke. This later becomes a significant plot point that starts the Seapony Arc.
A Child Shall Lead Them: The Changeling Queen, Imogen, is a tiny little filly about Woona's age. Unfortunately, by the time she meets Woona, she had been overthrown by her treacherous regent, Exuvia, and was forced to go on the run.
The Chosen One: Woona is predicted to unite three artifacts to save the moon from a great evil. The prophecy even calls her 'the Chosen Woon'.
Cloning Blues: Dark Woona is dead set on returning to the moon and defeating the Woona who continued the story after she was launched into space. When Dark Woona returned in the main comic, she began to enact her revenge on the entire population of the moon under the guise of Nightmare Woon.
Confusion Fu: Woona tries this during the Final Battle against Dark Woona, but it's subverted when most of her efforts are still thwarted.
Conveniently Interrupted Document: At one point, Woona discovers part of a note that tells her where to find a certain key, along with "soon" and a few partial words. Later on, she finds the note's missing fragment along with the aforementioned key. While the complete message is now clear to the reader, Woona had "already used up all of [her] deductive power for today" by that point and literally cannot put the pieces together.
The Key is in the shell. Come back soon. I miss you. -Celestia.
Curbstomp Battle: Pretty much any time thus far that Woona tries to actually fight Dark Woona, she's received one. The first time she was cocooned with Evil Jam and the second time the poor thing got blasted off a cliff.
Cute Little Fang: The friendly (if nervous) Changeling filly, Imogen, sports one of these.
Darker and Edgier: While not extremely dark, the final arc is shaping up to be more serious than the earlier parts.
Dwindling Party: Non-fatal example. Woona's group gradually dwindles (either from members leaving voluntarily or being forcefully separated) while leading up to the climax. They all come back for the Final Battle though.
Easily Forgiven: Everyone seems to forget about Luna trashing half the Seapony palace and attacking the prime minister after she defeats Dark Woona's giant octopus.
Emoticon: It is fairly common in both the user instructions and some of the author notes.
Emotion Eater: The Changelings, though their version is rather benign; they feed on their queen's love for them, and she in turn is sustained by their love for her.
We find out later that Exuvia stole one of the ancient stones Woona is on a quest to find from Dark Woona, who attacked to get it back.
Eyepatch of Power: One of the batponies has one after Woona's Cartographer's Banana got suck in his eye. He doesn't really need it considering that both of his eyes are fine, but for some reason he keeps wearing it.
Face Heel Turn: Subverted. Discord tries to trick Woona into thinking her friends have done this.
Ironic Name: Despite their lifestyle, the bat ponies all have names that sound bright and cheerful. The Lunar Maria, on the other hand, often have Awesome McCoolnames in spite of their graceful appearances.
Painting the Medium: Quite a bit of this happens in the final arc. First the supportive narration and commands start fading away as Woona's positive attitude is drained by the smooze she's wading through. Then once this is fixed, the narration gets creepy echoes and a malevolent attitude in the background.
The font used on the blog to transcribe the narration from the image changes, and several taunts are scrawled around the narration text and even on the margins of the screen. Starts to border on Breaking the Fourth Wall when Discord lashes out so violently that he breaks the question bar at the top of the panel.
"You suddenly become aware of a strange sensation, almost like you’re being…watched. As though all of your movements thus far have been silently recorded and judged, all for the entertainment of thousands of anonymous strangers."
Reasonable Authority Figure: The queen of the lunar ponies is very understanding when Woona (who's only a filly, after all) throws a Royal Temper Tantrum on seeing Blueblood has once again beaten her to the punch.
Save Both Worlds: It's eventually revealed that Woona's quest was to collect three of the six Elements of Harmony to stop Discord, who has been threatening the denizens of the moon through Dark Woona. Not only is the moon at stake, so is the earth.
The Reveal: The story actually takes place during Discord reign, Dark Woona was simply his puppet, and Woona was sent to the moon to retrieve half the Elements of Harmony (the Relics) so he could be beaten.