Twilight completely confuses her friends near the end of the story by answering all 22 of their questions from memory before they could ask. Some of them are easy to figure out, but some of the later ones get into Noodle Implements territory.
Twilight: A time loop, three hours, whenever I die, changelings, Chrysalis, I think about a month, somewhere around a hundred, yes, yes, no, 5:57, all of them, yes even the squirrels, Spikeís fine, no just me, you donít want to know, the Elements of Harmony, I donít know, yes, no, yes, and three tea kettles.
The newly ponified Butterscotch somehow manages to bond with Twilight over the fact she had probably beaten him to death with a baseball bat in alternate timelines. Also, apparently potatoes taste like hubris.
During the final chapter, Celestia asks Twilight for some assistance. When she agrees, Celestia levitates over a stack of menial form and paperwork roughly twice as tall as Twilight. Her response in the narration?
Twilight: I love her so much sometimes, I don't even know how to properly express it.
Twilight discovers that she has been outed to the entire town by a parrot that Fluttershy was petsitting.
Azalea: Already? I didn't know this felt that good.
Twilight: No, I mean I'm going to lose the-
(They plunge into the lake, and swim to shore)
Twilight: Don't say it. Don't even think about saying it.
Azalea: Gee Twilight, you really know how to get a mare all wet.
This scene gets hilariously referenced in Changing Lives: earlier that evening, Lyra tries to console Azalea with a poorly thought-out metaphor.
Lyra: Hasn't anypony told you that there are plenty of fish in the sea? You'll just have to fish up another one. Just be patient, keep your eyes open, and when you see one that you want you reach out and grab it with both forelegs and hold on as tight as you can.
Blossomforth: You've never actually seen anypony fishing in real life, have you?
Lyra: Well, it's obviously a metaphor. It's not like she's going to literally jump into some pond and come out of it with her soulmate. That would be ridiculous.
There's an extra layer of funny, unintended by the author, when you remember that at this moment Twilight is on a date with a mare with a fish cutie mark.
A Stitch in Time, all the narrative of the chapter 7 (due to Pinkie taking over the narration).
Twilight's Spock Speak analysis of how attractive Applejack is, followed by her horrific attempt to pick up the waitress.
AJ then says that the flirting went better than she expected. When Twilight mentions that the only way it could have been worse was if she somehow lit the restaurant on fire during the attempt, she does not disagree.
In Changing Lives, Scootaloo's lengthy argument with Elizabeak, who can commnicate only in "Squawk", over whether or not to poison Cloud Kicker to keep the secret that both are former changelings.
In the subsequent conversation, Scootaloo's blunt admission to having slept with Cloud Kicker and Algae Bloom when she was a changeling. "Well thatís a pair of mental images concerning Scootaloo I never needed."
Immediately preceding this, Cloud's reaction to learning that Algae Bloom is better in bed than her, albeit still useless to a changeling because she doesn't care about anypony she sleeps with.
Rainbow Dash's reaction to Cloud and Azalea explaining the weather vane trick.
A meta-example from Eakin's blog: a review ofEdge of Tomorrow, written as if the film was an actual adaptation/ripoff of Hard Reset, referring to Tom Cruise's character as Twilight and Emily Blunt's as Luna. Perhaps the best part is the last line, "I just wish they hadn't cut the scene with the weather vane."