Key targets are the people you are sent to assassinate. The game always provides a secondary way to do things that are non-lethal. Take the non-lethal route for every mission with a key target. There are only 4 missions like this in the game.
Mission 2: Campbell
Make sure not to poison or kill Campbell. Instead, knock him out. Find the branding instructions (your objective marker will show you) then take him to the room the game shows you next. You must get the branding iron in the same room and then brand him.
Mission 3: Pendleton Twins
You must meet Slackjaw and finish both of his side missions. Once you do so (without bothering the twins whatsoever), he will take care of them in a non-lethal manner.
Mission 5: Boyle Sisters
You have to find out which sister is your target (whom is Lady Boyle). They are all wearing the same thing but in different colors. Inside the party, there is a guest who is in love. He does not want you to kill her and will tell you what she is wearing. His name is Lord Brisby. He is wearing a mask and is in the room with a ton of trophy heads from various animals. Talk to Lady Boyle and just choose that someone is going to assassinate her and she will lead you somewhere else where you two can be alone. After that, knock her out and delivery her to a boat.
Mission 6: Lord Regent
In this mission you will finally get inside the building that has the broadcasting tower (the voice over the intercom you have been hearing all along). Talk to the broadcaster to get the alternate method of taking care of business. This one is very easy, just steal the audio and deliver it back to the broadcaster.