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It could be a tie between the Borg Queen, 0 (See the Books), Nero, Ghrath or Annorax.
The Borg Queen basically enslave trillions of being from thousand of species and stole their own will and individuality. But they thought it was for your own good, "Bring Order to Chaos" and that snazz.
0 tested an unknown number of species, changed the rules, and he eventually destroyed almost all of them except for Q and the Calamarain.
Nero held Spock responsible for destroying Romulus, even though he tried to save it. He then used red matter to destroy Vulcan and killed a dozen of his crew members that wished to return to Romulus. However Nero didn't kill trillions of people.
Annorax was willing to remove entire civilizations from the space-time continuum to help his species and to undo his mistakes with his weapon. This could lead into an entire discussion. The most evil man must work by doing anything to help themselves to their own ends.
Ghrath in the Enterprise episode "Storm Front" is willing to disrupt the timeline for no particular reason but to become better than everyone else, causing the Temporal Cold War in the first place. This would be a disaster for all sides until Enterprise thwarted the temporal conduit which was under construction in the 1940's.
The Xindi don't count because they were being manipulated by the Sphere Builders, and they were just an invading army. They were from another universe, and one couldn't survive in the other universe. It was indeed the only way for them to get control of the galaxy; they were and will be just an invading force.

Anyone is allowed to edit this with their thoughts, but don't delete what I wrote, it could be useful.

Given the list offered, the Borg Queen most likely wins (I admit, however, I don't know anything about 0), due to the fact that there is no motive for her actions besides the advancement of the Borg. Nero was attempting to bring justice to the destruction of Romulus, Annorax was trying to revert his lost wife. There was no loss, no motivation for the Queen. Only pure gain for her and the Borg.

I think Gul Dukat was pretty bad, not only for running the brutal Cardassian Occupation of Bajor but also for trying to destroy the planet by releasing the Pah-Wraiths.

The question was who is the most evil man in the galaxy, so by definition, it can't be the Borg Queen. Nero wasn't any more evil than the average Star Trek villain. Yes, he destroyed Vulcan, but it doesn't matter because that' s in an alternate timeline. Annorax wasn't exactly evil, but he had pretty much lost his mind. He probably didn't see what he was doing as murder, as he was not killing anyone, just erasing them from history. The aliens in Storm Front were willing to change the timeline to help them, but plenty of "good guy" characters have done that, especially in Voyager. Therefore, the most evil man in the galaxy is Gul Dukat, who led the brutal occupation of Bajor, and started the Dominion War, which was probably one of the worst wars in galactic history. He also tried to take over the entire quadrant by allying himself with the pah-wraiths, which are like the Bajoran devil, but he had completely lost his mind at that point. If woman, or genderless beings count, then the Borg Queen is the most evil being in the galaxy, with the female changeling, who casually ordered the genocide of the entire Cardassian population, coming in a close second.

In my opinion, it's Gul Dukat. Yes, the Borg Queen was bad, and yes, Nero was bad, but I'm with Dukat

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