Some fans feel that creating original animation for the videos ruins the whole point of AMVs, while others find them just as funny and creative as any other fan-made material.
The NSFW clips. Some fans love them and think they are hilarious, others feel they go to far and betray the spirit of the show.
Harsher in Hindsight: One that happed even before it was released!VII has a parody of ProJared, several months after the revelations that cost both his position with Normal Boots and his reputation. Many commenters have noticed that the skit had really bad timing which even the credits of VII itself admit.
The Animaniacs sequences in II were funny to begin with, but were made even more fitting with The Hub's acquisition of the aforementioned series.
Additionally, the first of them is "Boingy Boingy Boingy" set to Apple Bloom bouncing on a jumping Big Macintosh. Pinkie Pie would actually recite that line in "Games Ponies Play".
Anthology II has a PMV sequence with clips of Rarity set to "Diamond In the Rough". Fast forward to 2014, and Rarity would refer to the Diamond Dogs as "diamonds in the rough" in the "Player Piano" Rainbow Rocks short.
Also in VI, an animated skit has Trixie exclaim "I HATE MY DAD!" A later episode would all-but explicitly introduce us to Trixie's father, who, according to Word of God, may very well be a deadbeat dad.
Much like the the series that inspired it, Ponies would also end at 7 entries.
Nightmare Fuel: "Stephen King's Equestria Girls" in Anthology III. Watch it here, but if you don't want to, it involves Human Twilight and Fluttershy standing around with a low-pitched horror chord in the background. Then, an arm comes out of Twilight's mouth, sucks Fluttershy's head until she turns grey, and the rest of her body falls off.
From that same video, there is a recreation of the cursed tape from The Ring. Think that tape would be less scary with ponies? You'd be wrong. So very wrong.
In Ponies The Anthology II there's a segment of the Time Machine from 2002 where Hartdegen arrives in 2037 and gets arrested for safety purposes. A little bit scary right there, until he looks up in the sky and sees the broken moon descending down on Earth, but Nightmare Moon is flying through the sky, laughing...
The opening to VI is an homage to the beginning of 28 Days Later and that ends with a creepy replication of Celestia set to the brief Bible passage at the end of "The Man Comes Around". It works to surprising effect.
Tough Act to Follow: The very first Anthology video is a classic piece of Brony fan work and an iconic part of the fandom's humble beginnings. Many feel that the others, though not bad, have a few good moments but are weaker overall.
What Do You Mean, It's Not for Kids?: Due to the use of My Little Pony it's not uncommon to see parents letting their kids watch the anthologies online or take them to panels showing them, not realizing that the humor in them is often completely not for kids.