OK, I'll start with an example from "Equinox." (I'd better save the subject of Tuvix for Guy Gardener or some one equally eloquent on the subject).
Janeway tortures Crewman Lessing to get intel on Ransom, against whom she has a personal vendetta. She confines Chakotay to his quarters for stopping her and for telling her that torture is wrong.
That's because Chakotay's a bitch.
She tells the aliens that if they'll stop attacking Voyager she'll deliver the Equinox to them. When Tuvok points out that will be certain death for the Equinox crew she threatens to confine him to quarters too.
She was furious, but wouldn't have actually done it.
See also Captain Archer, who tortured a space pirate in an airlock, bombed an unarmed Xindi colony to buy some time and later stole a random ship's warp core standing them in the Expanse...
But I'd say all that (excepting the Xindi bombing, where he could have sent a squad of MACOS to disable them) was justified, considering the circumstances.
Then there's what Sisko did when going after Eddington, attacking planets with bioweapons
just because Eddington made a fool of him earlier.