Tom Robinson was on trial for his life. After he was convicted, Atticus planned to file an appeal, but Tom was shot to death by prison guards before that could be done. Tom didn't plan some clever escape; he seemed to have simply broken emotionally and just ran, blindly. Tom's death caused Atticus great pain. He delivered the news personally to Tom's family, and was especially affected by Tom's death because he believed he had a good chance on appeal to win a new trial for Tom. Atticus was still fighting for Tom when he died.
The children, especially Jem, were affected by Tom's conviction. Jem could not believe such an injustice could have occurred; he was angry and hurt. Following the return of the jury's verdict, Jem cried bitter tears. Tom's conviction made Jem less idealistic and more cynical about human nature. Unlike Scout, Jem no longer believed that people are all the same. He had become aware of evil in the world.
Many of Atticus' neighbors became critical of him for defending Tom. Bob Ewell was so humiliated by Atticus in court that he swore he would get even; Ewell's hatred for Atticus led him to try to kill Jem and Scout, which resulted in his own death at the hands of Boo Radley.