This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Digimon Tamers
"Running away from destiny...?"
Dark Lizardmon's fate: It was captured by Hypnos, interrogated under torture and literally torn apart for analysis while fully conscious after Yamaki was done, in a process that actually looks more painful than the equivalent, that is to say an autopsy on a living human. Not to mention that this is a close up to what Shaggai/Juggernaut does to it's victims in episode 14.
An early warning of things to come, episode 14, where the dying screams of the Digimon deleted by Shaggai/Juggernaut can be heard. A tamer version of Homeworld cataclysm's corruption by the beast.
Everything that happened to Juri after Leomon died is pretty creepy. So much so that Juri in general might just become Nightmare Fuel for people upon re-watching the series now that they know everything about her.
Her creepy hand-puppet might have already been this.
The infamous scene in episode 47, pictured above, where the audience is treated to a Mind Rape sequence in which Juri is forced to relive her mother's death. Taken out of context, it could easily be mistaken for a scene in an adult horror anime. To make matters worse, this goes on for at least an entire week.
As scary as Dark Evolutions are, Megidramon definitely takes the cake. It certainly doesn't help that its name is derived from the words "Megiddo" and "Dragon", considering that Har Megiddo is the mountain, where the apocalypse is (according to the bible) going to start. Har Megiddo has later been given its more popular name, "Armageddon". In other words, Megidramon's name is closer to original idea of the end of the world than "Armageddon". It doesn't help that before it Takato is practically SCREAMING about how he is going to make Beelzemon suffer for killing Leomon.
Takato screaming in terror inside Gallantmon's mind when he's about to be killed by Beelzemon.
The Body Horror Beelzemon undergoes after absorbing Taomon and Rapidmon's data. It involved Beelzemon's shoulders bulging until parts of Taomon and Rapidmon started protruding out of his skin with Beelzemon clearly in pain from the experience. Surprisingly enough, Saban kept this part intact, completely unedited.
The reason he had to do this was to avoid a brutal death (even by standards of the show) by being eaten alive by Megidramon
Megidramon itself. While reminiscent of SkullGreyMon, Megidramon's worse. It is nothing but an animal that destroys and devours without hesitation. It doesn't even speak, which most Digimon with a conscious have. Remember that this came from Guilmon, all because of Takato's rage and desire to kill.
Not to mention the process of digivolution itself was so drastic that it began to cause issues in the Human World too. If he hadn't devolved back down how much damage would Megidramon have caused to both worlds just through his existence alone?
Mephistomon dropping his human disguise in Battle of Adventurers, specifically the part where his human head retracts and his normal one bursts out.
Terriermon > Gargomon is especially bad because he pulls an expression during it that suggests he's in a lot of pain during the process. He squeezes his eyes tight shut as his skin peels off, and grimaces in pain as it reassembles itself onto his form. Ouch!
Cyberdramon's fight against Majiramon. At first Majiramon has the edge against the other Digimon, but Ryo turns the tide by using a special card to make Cyberdramon incredibly huge. With his newfound size, Cyberdramon is easily able to crush Majiramon's head and destroy him. The other children are visibly shocked afterwards.
The concept of "loading" Digimon can be horrifying. When a Digimon dies or is destroyed, its body becomes pure data and can be absorbed by the Digimon that defeated them, in order to become stronger. This makes every Digimon, even the ones we like, a cannibal. Later on, most of the Digimon stop loading the data of other defeated Digimon, though.
Can be more (or less maybe, I don't know how you think of things) horrifying when you think them turning their enemies into experience points to level up
You wanna know how Makuramon dies? By having his head crushed in Beelzemon's hand like an egg, screaming all the way through. Just imagine how horrifying that would have been if the show didn't run on Bloodless Carnage...
Beelzemon's near-death at the hands of the D-Reaper. How do you kill someone practically Made of Iron? You impale them with dozens of knives. They only show the silhouette of this, thankfully, but the sheer brutality of it makes this less of a comfort and more a necessity.
Digimon who get badly wounded usually regress into a lesser form. The notable brutal beatings in this show usually only knock someone down one level. Beelzemon was so badly wounded, he shot down three levels into Impmon. Just how painfulwerethose wounds?
Early example: Yamaki manages to confront Jen in the park when he's alone and when Jen won't tell him what he wants, Yamaki physically lifts him off the ground. Though Jen makes it out of the mess unharmed, he's obviously scared and at the time, there was no indication Yamaki wouldn't use drastic means to get what he wanted.