One of them would be the Borg...
The Borg (sounds Swedish) didn't see themselves as evil or believe that their mission was unjust. They wanted to add other civilizations to their own, making both sides better. The Borg did not have the problems most civilizations have such as crime, starvation, jealousy, etc. Who wouldn't want that?
Another good example is the Emperor...
The Emperor wanted to bring order to a chaotic galaxy. Sometimes, the only way is with an iron fist.
The Reapers is one more...
Reapers were changed against their will. What they became was not their fault.
Any position can change depending on the perspective. People... or cyborgs... don't see themselves as evil They are doing what they think is best, twisted as it may be.