Each of these stories deals with the power of the "subconscious" mind.
Subterfuge is another potential connection, especially as it might relate to self-deception.
You could argue that "things are not what they seem" is a phrase applicable to all three texts.
The only theme that I can find to connect the three texts in question is how one's identity is shaped by the environment they are in. While this is a predominant theme in The Life of Pi, is can be loosely translated to fit into Macbeth and The Crucible. In Macbeth, Macbeth finds himself changing because of the prophecies. In The Crucible, John finds his life as something very different than what he believed it to be. In The Life of Pi, Pi discusses the ways which animals adapt to their environment.