I remember in Revenge of the Sith, when the actor playing Vader yells "nooooooooo", at what is supposed to be the emotional climax of the trilogy, the theater roared in laughter.
Not a line, but I saw Matrix: Revolutions in theater on opening weekend. During the 1-on-1 fight with Smith in the rain, there's a slow-motion shot of Neo punching Smith in the face. It's such bad CGI the entire theater burst into laughter. I'm pretty sure it was intended to be dramatic, but after seeing the latest Matrix movie and how tongue-in-cheek it is about itself, I'm not entirely sure anymore.