While the title of the movie Prisoners could obviously refer to all the different protagonists who have literally been imprisoned or held captive at one point or another (the girls by Mrs. Jones, Alex by Keller, Keller by Mrs. Jones,...), I wonder if there is any other deeper meaning of this title in relation to the plot of the movie and its characters.
I expect that if you really think hard enough, you can adapt prisoners to represent just about every character in the film.
In terms of physical captivity, Alex, Bob, Joy, Anna, and Keller were all prisoners at some point. But Keller is also prisoner to his pride, ego, and way of life. He is a prisoner of his own self-reliance and suspicion of everybody else. To add some additional symbolism, his father was also a prison guard.
His wife and son are conditioned dependants who are trapped by Keller's force of personality. The wife additionally prefers to pop sleeping pills than face reality.
The Birches are trapped by their complicity in Keller's plan and their rather submissive relationship with him. Once they condone the torture of Alex, they are unable to get out.
Alex and Bob are both victims and prisoners of the Jones couple. They are additionally trapped inside their mind and are continually trying to seek a way out, a way out of the maze that the Joneses have created for them. Just like the final maze given to them that has no solution, they are unable to do so.
I personally don't understand the motivation of Holly Jones and her husband. But I'm sure that you can concoct something out of the fact that they lost their son and spiralled down into a well of negativity and evil in their revenge against god.
Finally, we have Detective Loki who is trapped by the promises that he makes to the parents and his own past as a child brought up in an orphanage (?). He also has a track record to protect.