On the evening before Tom Robinson's trial, when a gang of men, including Mr. Cunningham, accost Atticus at the jail where he has gone to protect Tom Robinson (because he knew they were coming), there are some tense moments, and Atticus is clearly scared. He repeatedly asks Jem to take Scout and Dill home, which Jem refuses to do. By the time it's all over with, Scout has kicked one of the men who tried to grab Jem, and struck up a friendly conversation with her classmate Walter's father, Mr. Cunningham. This conversation seems to bring Cunningham to his senses a bit, and he orders the rest of the men to disperse. Once they are gone, Atticus turns and leans heavily on the brick wall of the jail, and it is apparent he is relieved, but also emotional at what Scout inadvertently did, for when she asks him if they can go home, "He nodded, produced his handkerchief, gave his face a going over and blew his nose violently."
The second time Atticus gets emotional is the morning after the Robinson trial; he gave Robinson an incredible defense, and the black community knew it, rising in deference to him as he left the courtroom even before a verdict was announced. The next morning, despite the guilty verdict, Atticus gets up to find an enormous spread of food brought to his family as a thank you from the black community, "enough food to bury the family" as Scout observes. Calpurnia explains that it is a token of appreciation for what Atticus did for Tom Robinson, and at that moment, "Atticus's eyes filled with tears. He did not speak for a moment. 'Tell them I'm very grateful,' he said."