List the places in the text where one can find examples that illustrate the dynamic of appearance vs. reality in The Merchant of Venice.

This particular play definitely has a theme dealing with the relationship between appearances and reality.
One simple illustration is when Portia dresses up like a man in order to argue Antonio's defense at the trial.
Another place to look is in Bassanio's character. On one hand, he seems to be in love with Portia, but it also seems like he is in love with her beauty and money. You could argue that he is truly in love with her, but you could also argue that he's a gold digger who is only interested in her fortune.
Another character that I think works well for this answer is Antonio. He seems like an honorable man; he puts up with Bassanio, and Antonio is incredibly generous with his money and forgiving of his friends. Unfortunately, Antonio isn't always as honorable as everybody gives him credit for being. Antonio treats Shylock horribly for no other reason than the fact that he is a Jew.
Finally, the contest for Portia with the three caskets exemplifies this theme: the nature of the contest is to discern between the appearances of the caskets and what they really contain.