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. 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.