While reading this question What was Frank? it reminded me of one scene in Donnie Darko that I especially don't get how it ties into the story or why it's even there. He is under hypnosis with his therapist and he reaches into his pants and starts masturbating. I believe he does this while telling his therapist he's thinking of her. Why is this scene important?
Honestly I think it has to do with what Donnie's personality is like. He often seems very cynical and void of emotion, except when his sister says he's a dick. He usually just observes things like a zombie of some sort. I think what the scene represents is another side of Donnie that most people wouldn't see normally. The psychiatrist is trying to break through like most normal doctors and understand Donnie. With the hypnosis and him coming out like that I feel it was almost a warning to her that if you want to dig deep into him, you may not like what you see. That I also feel is a metaphor throughout the movie. We can see it in the guru, the gym teacher, and other characters. They are one way when we look at them, but when you did deeper it may not be something we wanted to know in the first place.
She asked him about girls, and he said he met a girl. She then asked about school and his family, but he was stuck thinking about girls, and watching Christina Applegate on Married with Children. He never mentioned his therapist.
I do not know the significance of the scene other than to make him seem like a normal teenage boy.
I believe the scene is suppose to reflect Donnie's lust for Jena Malone's character Gretchen. Not only this however, but also how easily Donnie can be transformed by hypnosis. Donnie is very vulnerable to the powers of hypnosis and becomes more cynical as we see from him masterbating. Seeing what the hypnotist evokes from Donnie by accident can lead the viewer to see just what sins Donnie is capable of under the hypnosis of Frank.