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.
Even within the stories themselves, Prince Rainbow's role varies — sometimes he'll be against El-ahrairah, other times he'll help him with good advice.
Just about every one of Fiver's visions, Bigwig's encounter with the Shining Wire, and the poisoning of the Sandleford Warren, to name a few. The film tends toward either short and surreal (the visions and flashbacks) or realistic and gritty (all the violence portrayed in the present tense), while the book has longer descriptions. Pick your poison, and know this stuff can be disturbing to more than just kids.
Stoic Woobie: Blackavar pretty much defines the trope.
Tear Jerker: Painful tears in the film during the "Bright Eyes" sequence. Joyful tears at the end of the book, especially at Vilthuril's storytelling.
Fiver again, especially in the film and TV series. Then again, it's hard to imagine how an adorable little rabbit who is totally lost without his big brother and who suffers from violent hallucinations wouldn't be a Woobie. He used to get kicked around a lot apparently and the rabbits who follow him need quite some time until they believe he DOES see things. And after the fight against the Efrafrans very detatched from their world, probably an after effect of the powers and spirits he channelled. Just the type of wild rabbit you would pick up, cuddle and take home if you'd find him half tharn in a meadow.
In the novel, Pipkin, as well. Even smaller and weaker than Fiver.
In the TV series, Campion also fits the bill. Sometimes.
Woolseyism: The translations from Lapine are sometimes presented this way. For example: Bigwig's name in Lapine is Thlayli. The literal meaning is "Fur-head", but "Bigwig" is an even more apt way of putting it, since he's also a senior officer of the warren.
Film
Animation Age Ghetto: The reason why so many kids were traumatized by the animated movie.
Harsher in Hindsight: The cover of "Bright Eyes" that was recorded for this series was performed by Stephen Gately of the Irish Boy BandBoyzone. Most fan complaints over this were promptly silenced following Gately's death in 2009, and if anything, makes the song even more of a Tear Jerker.
The Scrappy: A lot of fans hate Primrose for being manipulative, self-centered, and good at nothing else.
Strangled by the Red String: Campion and Blackberry. In the season 2 finale, they meet very briefly and barely have time to speak to each other before Campion's apparent death and their consequential separation. Of course, they pine for each other, and all the other characters, who are strangely aware the two's feelings for each other, try to comfort them for their loses.
Which is sometimes Lampshaded by the narration, as when it's pointed out that rabbits feel no guilt or shame about using physical force to push weaker rabbits around.
Several. The Black Rabbit of Inlé, The Hole in the Sky, the Terrible Hay-Making...
The Hole in the Sky involves El-ahrairah hearing of the titular phenomenon and going in search of it. After losing a fight with a weasel and falling into an infection-driven fever, he unexpectedly finds it:
"Then he began to tremble with fear. In the blue curve of the sky he saw a great rent, a cleft which, he perceived, was an open, gaping wound. The two irregular edges were jagged as though it had been made with something blunt, something which had first cut and then ripped and torn. Here and there shreds of flesh, still attached to the edges, stuck out across the wound, obscuring whatever was behind. All that he could see in the suppurating depth of the wound was blood and pus, a glistening, viscous, uneven surface like a marsh. The edges were messy too, fringed all along with blood and yellow matter on which flies were walking. As he stared in horror, the dead body of a rabbit fell out of the wound, but disappeared as it fell."
What makes it even more disturbing is that Adams offers no explanation of what the Hole in the Sky is or what it means. It is, quite simply, a rabbit thing that humans would never understand.