From IMDB:
There were two scenes in the movie that were either cut or not given context, that deal with the fact that Stan Gable was a nerd at heart but was too afraid and ashamed to reveal it. Curtis Armstrong discussed the cut scene during an online interview where he praised Ted McGinley's acting; it shows Stan leaving the endless Alpha Beta party and going to his room, after which he puts on a pair of glasses and begins reading a textbook, but when one the frat brothers calls at the door for him to rejoin the party, he puts the glasses and book in a drawer and sadly walks out. This scene informs another sequence the ending of the movie, where the nerds triumph, Stan Gable was not sad for losing to nerds, but sad because he knew he was a nerd at heart and was not able to reveal it out of fear of being bullied and humiliated. In the third film, this idea is used for the film's final scenes, where Stan (who once again had been bullying nerds) tells a courtroom that he is a nerd himself and will no longer hide it; he even uses the phrase "come out of the closet" in reference to admitting this publicly./QUOTE]