"Am I Good Man?"~Into the Dalek
Clara's response to Twelve at the end of the episode summarize the Doctor best, he is not good nor evil. Most people see him as a superhero while there are episodes even arcs that have him shown as almost a monster but he tries to do what he thinks is best for the given situation. His decisions bring consequences that can destroy lives while at the same time, can also save the day. It is never an easy decision for him but he never regrets and I think that is probably one of the best traits he has when going through time and space.