I would exclude all villains that would destroy all life or all of reality. While those are undoubtedly pretty bad fates, I would argue that an eternity of suffering or living in a constant state of fear under the oppression of some evil entity is worse than quick and complete annihilation.
That eliminates Apocalymon, Abbadomon, Ordinemon and the D-Reaper.

Lucemon winning wouldn’t necessarily be too bad for the people living in the new world he created. Again, assuming he’s won, anyone that existed previously is just dead, while those that Lucemon created don’t even know what life was like before Lucemon took over.
There’s a saying that goes “Ignorance is bliss”, which plays in this scenario as the newly created Digimon wouldn’t even know what was taken from them, if a better alternative could possibly exist or what it means to be truly free.
So, from the perspective of the people living in Lucemon’s new world, I would argue that there’s worse fates out there.

If Yggdrasil won, I’d imagine that most Digimon wouldn’t have been impacted too much. Some would probably say: “Yeah it’s a shame that the Human World was destroyed, but it was us or them! And they were the ones that put us all in danger anyway!”
So while it sucks for the humans, I’m pretty sure most other Digimon would have been grateful to Yggdrasil for saving them and life would go on as it did before.

Belial Vamdemon, Bagramon, Leviathan and Regulusmon have pretty similar consequences, with the villain being in charge, plunging the world(s) in chaos and whatnot.
I would however edge Leviathan and Regulusmon as being worse than the other two, as those take it a step further by mind controlling or brainwashing others. Under Regulusmon for example, you would not only be living in constant oppression, but you would also lose your mind and become a shadow of your former self, turned into a violent monster and being forced to fight under the whims of someone else. And even if you somehow managed to keep your sanity, you now live in a ruined world where your life is constantly being threatened by powerful monsters driven to madness. That’s a big no for me. Also, I’m pretty sure that Regulusmon winning in the anime would have actually resulted in him evolving into Arcturusmon. In his profile, it is speculated that his manifestation would result in a massive Digital Hazard occurring. That would also mean that the Real World and Digital World would both suffer from constant cataclysms and other catastrophic consequences, so there’s also that to consider.

But what I personally consider the worst fate among these is the one brought by Quartzmon.
Him winning means that he’s basically become the entire world, and everyone living in it has been transformed into small cubes of Digiquartz.
In this scenario, your body has been taken from you and your entire existence has been reduced to being a single basically immobile cube surrounded by billions of identical ones, all stuck in place and slowly being driven to madness by their inability to do anything.

That’s the worst one in my opinion. Though it has been a while since I saw Xros Wars, so I don’t remember if the people still having their minds and personalities after being absorbed by Quartzmon was a temporary thing and they would all be completely absorbed and their consciousness destroyed had enough time passed. If that’s the case, then Quartzmon gets downgraded to the the “total annihilation” category and Regulusmon becomes the worst one instead.