Quite clearly there are a range of possible responses to this question, and in a sense there are many important passages to this excellent novel, and trying to pick one is a difficult choice to make. However, one of the important passages to my mind as I read the book comes in Progress Report 13, when Charlie and Algernon go to Chicago with Strauss and Nemur to be "exhibited." Note the way that this passage conveys Charlie's feelings about being an exhibit.
We were the main attraction of the evening, and when we settled, the chairman began his introduction. I half expected to hear him boom out: Laideezzz and gentulmennnnnn. Step right this way and see the side show! An act never before seen in the scientific world! A mouse and a moron turned into geniuses before your very eyes!
This passage is important because it displays how upset Charlie is at being objectified and viewed as an object of scientific curiosity rather than an individual in his own right with his own contributions to make to the discussion. Note how his identification with Algernon, as another laboratory rat, is strengthened by the way that the mouse and the "moron" are linked in the way he imagines that he and Algernon are appearing in a circus freak show. Charlie believes that he and Algernon are there as entertainment and imagines the chairman as a touter in some sort of carnival, getting people to pay their money to see Charlie and Algernon. Refering to himself as a "moron" highlights this incredibly impersonal and offensive way in which Charlie believes he is being treated.
This quote is also important because it marks the way in which Charlie reaches the height of feeling objectified and how this feeling of alienation gives rise to his own assertion of his independence, for it is after this that he decides to run away with Algernon, leaving the conference and Strauss and Nemur behind.