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.
Burizalor (Freeza's Expy) definitely fits the bill. He is responsible for destroying the Northern Realm and killing many innocent lives to supplement his arrogance of being the strongest in the universe. He personally crossed the line to Taichi after he kills Sora, in which he made a grave mistake of the birth of Omega X to defeat him.
Virus (Cell's Expy) is another. Although programmed to kill, he shows no concern over feeding many human and digimon lives to increase his power, and gleefully shows the restless souls of his victims while powering up in front of BanchoLeomon, Jax, Sonja and BlackWarGreymon. He will stop nothing to absorb Artificials Jax and Sonja in order to reach his perfect form. After achieving his perfect form, he began to hold a tournament called The War Games to challenge many heroes in inspiring terror to the universe. He then crossed the line when he killed Blackwargreymon, just to make Celesta X angry. Then attempting to blow up both worlds after spitting out Jax and Sonja. And NOW he's going to destroy everything, including the solar system! Also, his future self in Dimitri's timeline (and even the main one) mention that he killed Athenamon.
Although in Digimon Adventure that Datamon was just a revenge-driven villain, he's proven to be this in these fanfics. He's totally the cause of the creation of the artificials and Virus, and the one that leads to Dimitri's apocalyptic future. It implies that Datamon wants to destroy all life for the hell of it!
The Digital Warlord. Stories mentioned by X and his team say that he's a pure evil person. He is also an alternate version of Ken's brother, Sam.
Super-Reaper and Teen-Reaper are most likely to take the cake.