Arguably, the whole friendship between Charlie and the step-siblings. In the book, it is implied that a lot of people see Charlie as a weirdo, so he doesn't have any friends (anymore). Then, enter Sam and Patrick, who completely accept him, invite him to go to a diner with them just moments after he introduced himself to them, and treat him like a good friend right away. Seriously, this must have put a smile on the face of every one who ever had trouble fitting in.
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 spent most of the year ignoring her brother. She still knew him well enough to instantly recognize his intentions despite him not saying it directly, and acted immediately to try and help him.
Similarly, Charlie's conversation with his brother. The brother is coming home as an up and coming college football player, but he is authentically concerned with how his younger brother is doing, and shows real joy to find that he has made some new friends.
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. Then, after it's over...
Sam: ...I love you, Charlie. Charlie: I love you, too. (Sam, in tears, hugs him.)
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.
Great Uncle Phil's story about how, after learning his sister was in an abusive relationship for seven years, he got his friends from the factory together and beat him up in a bar to the point he was hospitalized and died days later. Even better, even though he could have easily gone to jail for physical assault, no one ratted him out, since all of his neighbors knew "that some things had nothing to do with the police."
Charlie: He said that if someone touched your sister or your mother, they paid the price, and everyone looked the other way.