4. The Clockwork Man
The Twelfth Doctor's first season had the "Am I a good man?" story arc, and this began with the ambiguity surrounding whether or not The Clockwork Man was pushed from the airship, or whether he fell in 2014's "Deep Breath." Having faced the Clockwork Droids before, and losing his friend and romantic interest Madame de Pompadour, The Doctor had a history with the robots.
The robots believed that The Doctor would not destroy them, and that he would show mercy in this moment. However, in the struggle between The Doctor and the Clockwork Man, the robot 'falls' to its death.
It's strongly implied that The Doctor acted on his darker side and pushed The Clockwork Man, and although it was for the greater good, this was definitely one of the Doctor's darkest moments, as he wasn't forced into killing the enemy before him, he willingly chose to do so.