In Winter War, Ise Nanao describes Aizen as "Something of a control obsessive. The sort of person who has to have everything exactly as planned, precisely as organised, every detail under their control... why are you looking at me like that?"
Haruhi rants about how she hates it when light novels go beyond 10 novels, or when her manga and stories are ongoing in Kyon: Big Damn Hero. In the source material, Suzumiya Haruhi, the author's at the 10th novel, and it's just the start of the characters' second year in high school. The author also takes the opportunity to prove, and launch a Take That against one of the theories in the WMG. Though, considering the prodigious length of the fic, it's entirely possible the rant was actually intended as self-depreciating humor.... And on closer examination, it seems Haruhi's only problem with series in the WMG is that she's not patient enough to wait for the next volume.
Also, Taniguchi mentions how he finds Konata's voice creepy to Haruhi. Haruhi and Konata are both voiced by Aya Hirano.
Light: I walk from one room to another with intent, hoping to find locked drawers and secrets. B had locked his bedroom door, which is to be expected from such a distrusting little shit. I found a spare set of keys in L's desk though, so it didn't do him much good to underestimate me. If I was B, I would have taken better precautions. I was excellent at chemistry and physics at school and dabbled in pyrotechnic devices.
The dreaded My Immortal has Ebony/Enoby/Evony claiming not only to be a Yaoi Fangirl, but to oppose homophobia. However, when she suspects Draco has cheated on her with Harry/Vampire, she promptly accuses him of having AIDS (or, as she spells it, "AIDs"). Also, she tries to insult uncomplimentary reviewers by calling them "gay fags".
And as far as the AIDS accusation goes, she regularly drinks human blood.
"Shego! How can you take this so calmly? The sanctity of my laboratory has been violated. My invention has been stolen. This is horrible," said Drakken. He waved his arms around as he ranted. "So you mean, just like we always break into other peoples' labs and steal their inventions? Or is this different in some way I'm not seeing?" asked Shego curiously. "It is different! It's different because... because this time it's happened to me," said Drakken.
In "Once Bitten, Twice Shy", Rarity tells Applejack that it's rude to stare, then goes right back to her binoculars so she doesn't miss any part of Twilight and Fluttershy's first date. It's specifically noted in the narration that she's oblivious to the hypocrisy.
In The Xenophile's Guide to Equestria, Twilight tells Princess Celestia that Applejack is talking about a pool on the outcome of Rainbow and Lero's friendship, and describes it as, "a terrible thing to do to a friend. As such I’ve put myself down for no more than three bits on the spread."
The DJ-PON3 Party: At one point, Trixie calls Vinyl Scratch a showoff. Honey Daring Do lampshades this, but Trixie completely misses her point.
Atlas Strongest Tournament: When the changelings realize that the "Spike" they've captured is a fake, one of them shouts "An imposter?! How horrible!"
In the story Fluffershy, Rainbow Dash finds out that the rest of the Mane Six are watching a porn movie because Fluttershy is on the box cover and calls them perverts. Rarity points out that Rainbow just admitted to owning three copies of the same movie (VHS, DVD and Special Edition DVD).
In Thanks Kyubey, there's a Running Gag of Kyouko being called a "fucking lesbo" for her interest in Sayaka. The one calling her this is usually Homura, who spends the rest of her time blatantly stalking Madoka.