Craig's Workshop
Craig has a workshop in he and Lotte's home where he works on his puppeteering. His workshop is a symbol of his escaping from the real world and his responsibilities and dealing with things by pretending to be someone else in the stories he creates with his puppets.
Hung Up
While Craig is creating a doll for Maxine we see that Lotte's doll is hung on the wall. This is a symbol that he has discarded his wife for the fantasy of being with another woman that he doesn't even realize doesn't like him at all.
Entrance
Craig finds the entrances to John Malkovich in the office and tells Maxine all about it. The entry becomes a symbol for Craig that he is valued by Maxine because now that he's found this she calls him and wants to create a business with him. It shows that he doesn't truly value himself.
Dirty Windshield
Craig picks up Lotte after her rendezvous with Maxine through Malkovich. We see that the windshield to the car is dirty and he wipes it with his hand to try and clean it. It's a symbol that his view in his life is not clear at this moment and he's trying to make it clear.
Dump Spot
After being inside of John Malkovich, the person inside is dumped on the side of the New Jersey Turnpike. It's a symbol that trying to compare oneself to another person, though it feels good while you are doing it, always takes you to a ditch on the side of the road.