Sex is a big part of the story, and it's implied (mildly for some) all characters encounter it at some point during the movie, without any actual scenes shown. It's implied that Sam has been sexually active since age 11, when she was first kissed by her dad's boss. Although she no longer randomly "hooks up," she and others state how in freshman year people would get her drunk and that she had a reputation.
Patrick, a gay student, tells Charlie his experiences. He and Brad have had a secret relationship, and we hear details about how Patrick would get Brad drunk so they could have sex. Charlie catches the two on a bed (clothed) just about to kiss passionately. We learn that Brad's father also caught the two at another point.
Patrick passionately kisses Charlie, then breaks down crying in his arms.
In Charlie's "relationship" with Mary Elizabeth, we see shots of them kissing, cuddling, and Charlie fondling her (clothed) breasts. On their first date, Mary Elizabeth tries to get Charlie drunk for sex, giving him a bottle of wine, resting her head on his leg, and pulling down her dress, revealing her bra. This fails when her parents come home.
Sam and Charlie kiss passionately a few times, and once, Sam rubs Charlie's leg, which makes him nervous (for other reasons).
While acting along with The Rocky Horror Picture Show, we see several boys cross dress and dance suggestively. Patrick, in high heels, a bustier, and garter belt, sits on Charlie's lap, caressing his face. Sam dances in a bra and panties, and lets Charlie touch her breasts. Charlie is stripped down to gold briefs at one point.
Patrick tells Charlie a gross story about a couple from the high school who sneaked out to have sex one night. They forgot condoms, and used sandwich bags instead.
It is revealed at the end of the film that Charlie was molested by his Aunt Helen when he was a child. Nothing at all is shown.
There is a brief mention of "blowjobs"