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.
Big Lipped Alligator Moment: Technically all of them are this, but skits like J.R.R.Tolkein Jr Jr stands out see why. This is actually invoked in-universe, as the narrator has no idea what he just watched.
The ending of the "Potter, You Fool" skit where Hermione committed suicide after being cyber-bullied on Facebook, even though Facebook didn't exist in the early-mid 1990s when the Harry Potter books take place.
The "Ballad of Gay Tony" skit where Cloud Strife talks about his fetish for crossdressing. In Final Fantasy VII, however, Cloud was forced by Aerith to crossdress against his will, but he reluctantly did so because he wanted to rescue Tifa.
A huge example came with a sketch making fun of the Challenger accident. The episode aired days after the 25th anniversary of said accident. Fans were not amused.
Many skits can become this for people by having the situation become disturbingly violent, particularly in the more recent seasons, with the Joker Execution in Season 5's Catch Me If You Kangaroo Jack being a more hated example for this.
The Toy Story 4 sketch. It involves Andy and his girlfriend having sex in his bedroom, much to the toys' horror. The worst part, however, is when Andy uses Buzz as a bong, irreversibly damaging the latter's brain. And Woody's the one putting Buzz out of his misery.
The NORAD vs. Santa sketch. Especially the ending.
Does nearly every single 80's Toon character skit have to be some variation of : 1 - Inexplicably Brought Down to Normal ; 2 - 80's type is glued to an Idiot Ball The Size Of Jupiter ; 3 - Horrific violation and/or horrific death, possibly followed by a horrific afterlife?
That's two more varieties of joke than 90's character sketches. Point 3- Horrific violence and/or death is the appropriate one, if you're wondering.
F***ing Google It, where they mock the fact that the Airwolf helicopter was turned into a flying ambulance and crashed into a mountain while carrying a little girl, killing all of its occupants and the gruesome history of Mighty Morphin' Power Rangers uncredited extra Skylar Deleon. They don't even play these incidents for laughs as much as say "Look! This really happened!" for little apparent reason.
Basically 90% of the sketches from Season 5 fall under this.
The ending of the "Goofy and Clarabelle" sketch, where Walt Disney makes a Nazi salute. Also the ending of the "Fun For All Ages" sketch where he mentions Aryans.
The "Celebrity Double Dare" sketch; even the writers themselves viewed that sketch as too mean-spirited, according to the commentary.
A season 4 sketch featured Dakota Fanning challenging Triple H to a wrestling match in John Cena's place, claiming she was only at the event to promote her new movie. The sketch debuted on a episode of WWE Raw, where Seth Green had placed himself into a tag team match with Cena & Triple as his partners, when he was only at the show to promote Robot Chicken as one of Raw's first Guest Hosts (Celebrities appearing on the show in order to promote their latest works, or because they were Local Sporting Heroes).
The "Transporter 3" sketch, released a few years before the actual Transporter 3 came out.
How about the 3Fast 3Furious sketch? There's now six movies in the franchise.
The "Lizzooney Tizzunes" sketch, where Daffy says that he and Bugs are going to appeal to the demographic by being more hip. The following decade after this sketch premiered, The Looney Tunes Show came out, where Bugs and Daffy are roommates living in a suburb and plenty of pop culture references and Getting Crap Past the Radar moments are in there.
In the season 6 Thomas the Tank Engine sketch "Blow Some Steam", Harold the helicopter flies through a railway tunnel, and his blades hit the side of the tunnel wall, causing him to crash and explode. A year later, a Thomas episode aired where Harold did go through a railway tunnel, and his blades hit the wall (though with less deadly results).
All the sketches relating to Teenage Mutant Ninja Turtles become this when you find out that not only is Seth Green voicing Leonardo, but shortly after it was announced, there was a sketch with Greg Cipes reprising his role as Michelangelo.
Protect the environment.... OR I'LL FUCKING KILL YOU!
Oddly enough, they follow this up with something akin to a parody of this phenomenon, with the sketch going into a weird truTV-type commentary show thing where a bunch of D-list "celebrities" take affectionate potshots (and some not so affectionate ones, especially Master Shake's lines) at Robot Chicken itself. The first scene features Hal Sparks basically willing the "CAPTAIN PLANET" shout-nutshot combo to go Memetic.
There's a segment with Lil Hitler where he tells his teacher that he needs a Polish boy's desk. Cut to a Polish boy next to him, sweating. You'd think sweating wouldn't be funny, but when someone's sweating clay (or whatever that is), it really IS unsettling. This is also Nausea Fuel.
The Gummy Bear has...a rather horrifyingly painful scream for some.
The video in which The Mad Scientist kidnaps the Robot Chicken's wife.
Darkwing Duck being cooked alive in the oven with Gosalyn, his daughter, watching in horror. Then at the end, he is served to her and Michael Moore and is decapitated and Gosalyn's scream echoes into the credits!
Whether or not this applies to the second season has inspired many a Flame War.
Season 5 is almost universally agreed upon by fans of the show as the absolute low point of the series, since it seemed that the entire focus of that season was to be as blatantly offensive as humanly possible at the expense of actual comedy. See the Dude, Not Funny! entry above? The majority of the specific examples listed come from that season. Thankfully the creators got the hint, and season 6 has seen a massive improvement all around.
One sketch spoofing Pokémon had Ash wondering what it's like for Pikachu to be inside his pokeball. Except that Pikachu never goes inside a pokeball because he hates being inside it.
Goku carrying a handgun in the Christmas special. Guns of almost any caliber are inane, insane jokes in the DBZ universe. Goku as a kid kicked missiles and rockets back at the ones who launched them. Buu's puppy and the farmer who greeted Raditz in the pilot are about it for gunfire casualties in almost 300 episodes.
The fact they've occurred seems to have been bad enough to throw the Robot Chicken into the Trope Pantheon as the God of them. See the Shallow Parody page for more info.
Weird Al Effect: The series has become sort of a Weird Al Effect making machine almost on the level of Alice in Wonderland. It doesn't help that a fair portion of its audience has never seen the 80's cartoons it parodies.