The whole ending where Sam and Patrick show up for Charlie after going away to college and after Charlie's whole attempted suicide episode.
It is oddly heartwarming to see the complete horror on the face of Charlie's sister when she realizes he's going to try to kill himself, especially as she had previously been portrayed to sort of ignore her brother
Charlie's friendship with Mr. Anderson.
Charlie tells Bill that his sister's boyfriend hit her. Bill then tells their parents, who forbid her from seeing him. Charlie's sister tells him she hates him, to which he responds "I love you."
Sam telling Charlie that she wants the first girl who kisses him to be someone who loves him, from which she then kisses Charlie passionately.
A poignant scene in the film is the bit of purposeful Ho Yay between Patrick and Charlie: The former's just been brutally beaten up and rejected by his prick of an ex-boyfriend, and he laments to Charlie that he just wants to find a 'good guy' before kissing him. When Charlie doesn't reciprocate, Patrick instead just breaks down in his arms, sobbing, with an understanding Charlie comforting him like any good friend would.
Patrick: I'm sorry... I'm sorry...
Charlie: It's alright.
In the film, Charlie and Sam have been estranged for weeks after he kissed her instead of Mary-Elizabeth. Charlie saves Patrick from getting beaten up and doesn't remember what he did. Sam tells him, 'You saved my brother, that's what you did'. Charlie asks if Sam is scared of him, to which she replies 'No'. He asks, 'Can we be friends again?', to which she replies, 'Of course'. They hug.
Arguably, Brad thanking Charlie for defending Patrick following the cafeteria fight is a case of this. Even though the fight was largely Brad's fault, it shows once more that he really does care about Patrick, even if he's not allowed to show it due to social pressures.