These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Genius Bonus: In "The Great Rainbow Caper", Danny and Surprise get kidnapped by the Gizmonks, and proceed to destroy their lab from the inside. When they escape from it, they do so by getting inside a giant wooden horse. Sounds familiar?
Nightmare Fuel and Paranoia Fuel: Yes, again. Some people have reported to be frightened senseless by The Reveal that the flowers were escaped convicts. If that is what it feels like for a flower garden to be overtaken by invasive weeds...
The shadow-less ponies in "Bright Lights" advancing on Knight Shade. The angle they're shot at makes them look like zombies!
The Scrappy: With exceptions, most fans loathe Molly and Danny.
Villain Decay: Hydia and her daughters prove much less threat to the Ponies this time around.
Poesy crying over her dying garden in Fugitive Flowers. Seeing how much love and care she put in to it, to only have plants she thought were beautiful nearly killing all of her garden is heartbreaking.
The penguin king breaking down into uncontrolled sobs after accidentally freezing his son. Evil villain he may be, but he still had enough of a heart to love Edgar.
And tears of joy this time when it's shown his tears were enough to melt the ice and save his son. His look of sheer joy and the sound of him laughing for the first time just cements it.
The song "Oh, For a Rainy Day" from The Magic Coins.
Wangst: If you didn't feel that Shady's insecurities were warranted, then you saw her this way.