Is the Borg Queen more of a physical representation of the collective minds combined, or is it an individual who controls the rest of the collective? When the queen is destroyed, is she replaced by another who takes her place or reactivated in another body? How many Borg Queens are there, just one or several to lead sections of the collective? Could there be a Borg King?

When they assimilate you, the Borg claim that "we will add your biological and technological characteristics to ours." Technologists do this by stealing your memories of planes and science, but what about biological ones? Do they mean that they will control their bodies or that if they have something special they will use it for a specific task?

Q himself told Q Junior not to mess with the Borg. He looked a little nervous about it, but it could be more because of the idea that the Qs are punishing him for it (as they did to him) than the Collective directly. Another theory would be that the Qs aren't actually all-powerful. Though they act like gods, they're actually a representation of the galaxy's most advanced civilization. The Fleet sees them as they would see a civilian from a less developed prewarp culture. But just as such a civilian could harm a member of the Fleet, the Qs could be threatened, as with Elaurians like Guinan to Q, who were assimilated by the Borg. Does that mean the Borg know the weaknesses of the Qs?

Finally, the Borg do not yet have an explained origin. We know they are in the delta quadrant, but they should not have originated there. The Borg could come from another galaxy, another timeline, or another universe. If so, couldn't the Borg of all realities form the same collective?