When Tam Lin tells Matt that there is no real difference between a clone and a human and that Matt isn't really inferior. For the first time in his life, Matt realizes that he's just a normal person rather than the freak everyone sees him as. Especially since it was part of their parting exchange before they left each other for good.
Matt and Maria's exchange just before they press the button in the secret passage that might kill them.
Matt: I love you.
Maria: I love you too. I know that's a sin, and I'll probably go to hell for it.