The motif of questionable motives
The masked vigilantes are not necessarily good people. Manhattan is accused of poisoning his friends and colleagues with radiation that is giving everyone cancer. Rorschach may have murdered a reformed criminal in cold blood. These are anything except typical superhero types. They're more like real people with some good and some bad.
The motif of hearsay
Another way of addressing the issue of justice in the story is that many times, people are imprisoned for alleged offenses, and people are killed for tenuous reasons. The vigilantes often have to defend themselves from critics. See, in regular superhero stories, the villains are obviously to be defeated, but by showing how hearsay interrupts real justice, the story rejects a simple black and white sense of who deserves to be punished.
Doctor Manhattan as a symbolic character
Manhattan is a fascinating character. He is unquestionably helpful, but there is also a sense in which his presence on the earth might literally be killing the very people he is supposed to help. This is likely an allusion to the original "Watchmen" story, the ancient extra-Biblical text The Book of Enoch.
The allegory of fatherlessness
It's not a mistake that the story takes place in highly urbanized New York City, and also one of the main characters suffers the problem of fatherlessness. When Juspeczyk finds out her father is the murder victim Edward Blake, she realizes that she'll never meet him. This is an analog for the real fatherlessness of real communities in highly urban, low income places in America.
The allegory of Rorschach
A Rorschach test is an association test where the test subject is asked to draw conclusions from incomplete data sets to illustrate their subconscious processes. Rorschach himself does the same thing. He is like a litmus test for real justice. There is a man who was a career criminal and an overtly evil man, but he left his ways behind him and started over. Then Rorschach decided that wasn't good enough (allegedly) and he killed him, and therefore the question of Rorschach's judgment is raised. The meaning of his imprisonment is that superhero mentalities are flawed, because no one is a good enough judge to execute true justice.
