One of the best sections of the novel to talk about appearances versus reality is actually the very end, which is when Scout tells Atticus about a book she has just finished called The Gray Ghost, where a character is wrongly accused of a crime and pursued. Note what Scout says to Atticus:
"When they finally saw him, why he hadn’t done any of those things... Atticus, he was real nice..." His hands were under my chin, pulling up the cover, tucking it around me. "Most people are, Scout, when you finally see them."
There is a clear link here to appearances versus reality and in particular to Maycomb's opinion of characters such as Boo Radley and Tom Robinson. Both characters were thought to have committed terrible crimes by society, but the reality actually proved them to be innocent. This supports one of the central themes of the novel, which is summed up in the wise words of Atticus. We all have to strive to "finally see" people not the way that society assumes they are but how they really are.