ChrisChan was a recurring background character. Usually didn't do much, but he is featured prominently in an episode where the Tara Strong pony, Twilight Sparkle, goes on what is essential a Brony Convention Cruise, and gets harassed by her asshole fans. It's
clearly based on Bronies, one of at least two episodes that criticized the fandom (the other one being the Patton Oswald episode), and iirc it was written shortly after Tara got into some Twitter fights with Chris. I don't know if the Chris reference was planned all along by the entire crew, or if the Chris reference was just an easter egg thrown in by a memelord animator, but...
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Chris, Barb, and Robertchu. In happier times...
The War episode was an alternate future episode where one of the villains "wins", and all of Ponyville turns into a grimdark, futuristic warzone. If you follow the Brony fandom for any amount of time, you'll discover that grimdark, futuristic warzones are one of the most popular settings for fanfics, so this episode was pretty much just brony fanwank.
The DA fetish episode, I don't remember when it happened exactly. But there was an episode, or maybe a string of episodes, where the writer and animators were
clearly trying to pack as many weird fetishes in as possible; things like inflation, smelly feet sniffing, age regression, vore, and hypnotism.
And the Fluttershy episode was one of the more egregious "Plot" episodes. FiM had numerous episodes that featured Fluttershy fanservice (the one where she turned Goth, the one where she was a bee, the one where she changed into a vampire), but the episode where she used a Potion of Gender Change so that she could pretend to be a guy and sing vocals for another pony to lip sync to, was notable for having multiple, obvious ass shots. Not gonna post screencaps of Fluttershy twerking, but that's what happened.