Adventure 01 - Myotismon. He starts out shadowed, already giving sinister vibes, he proves to be more malevolent than Devimon, his arc is the longest, he killed Wizardmon, and the scene where he is finally destroyed gives an immense sense of satisfaction, plus with Champions of the Digital World playing. (Probably my second favorite in all of anime, next to Frieza)
Adventure 02 - Again, MaloMyotismon, as the whole thing traces back to him and it seems like he has won, but Davis turns everything around by saying he wants to work at a noodle cart, and he is permanently (unless you go by Tri as canon) destroyed in rainbowfied glory.
Tamers - Harpymon. She's just a Monster of the Week (as opposed to D-Reaper, who is a close second), but Renamon destroys her with her tail (or more precisely, Kyubimon destroys her with her tails). I can say in all seriousness that Renamon takes out an enemy with her tail, combining two of my favorite elements, and with my favorite character of the series no less. Plus it occurs when she and Rika get back together after being divided for most of this episode and the entire previous episode.
Frontier - Lucemon, as the overarching antagonist, with a unique and spectacular effect for the series. A close second would be Cherubimon due to the spectacular rays of data and a somewhat beautiful moment where his spirit is purified and reunites with Seraphimon and Ophanimon.
Data Squad - Kurata the whole way. (There's only three permanent deaths of evil characters to choose from and to me he is the obvious choice) He's the overarching antagonist of the series, even though his arc isn't the last, the last arc traces back to his final action. Not to mention all the good Digimon he permanently killed. Just about everything he does makes this the darkest Digimon series, and while humans rarely die in the series, he is one such occurrence.
Fusion - Lord Bagra. As the main antagonist of the whole series for two seasons, and a Dark Lord, he finally meets his match in a swordfight with Shoutmon as x7 Superior Mode, and is stabbed, which is epic. He then disintegrates into data.
Tri, I never saw (nor do I go by as canon), and from what I hear there'd be only two to choose from, MetalSeadramon and Machinedramon.
Adventure 2020, I haven't seen as it hasn't yet been dubbed, but I did peek at the end of the Millenniumon fight and it looked pretty awesome. But I could decide when I see it. (If it's dubbed in my lifetime, but dub is on its way)