Not to mention "Heroes" by David Bowie as the "tunnel song."
Manic Pixie Dream Girl: Arguably Sam. Her mania manifests as a preference for unsafe seating arrangements in trucks and the music of The Smiths. Also she used to bang a lot of guys. Sam is a little less over-the-top than most uses of this trope, possibly in an attempt to ground the fiction in reality. She helps Charlie get over his issues and learn to live life to the fullest. Also literally has a pixie haircut.
She's also a lot more well rounded a character than most examples of this trope, having her own goals and desires outside of her relationship with Charlie. She actually needs his help with her SATs. And knowing her doesn't really solve Charlie's problems like in most instances of the MPDG.
However, Charlie's perception and treatment of Sam may show he sees her as a MPDG. From a narrative perspective and based on her scene near the end when she tells him to make himself happy, she could be seen as an aversion or a subversion of this trope.
Nightmare Fuel: Charlie's phone call to his sister is one for anyone who's ever had a sibling, friend, or relative with emotional issues.
Reality Is Unrealistic: Many people complained to the author that it was implausible that the main characters, who are so proud of their broad musical tastes, wouldn't be able to identify "the tunnel song." The author protested that it actually happened to him as a teenager in the early 90s. Ironically, "Heroes" was repopularized by The Wallflowers a few years after the story's mid-90s setting.
After Brad's goons beat up Patrick and Charlie intervenes, Brad quietly approaches Charlie in the principal's office and softly thanks him for doing what he did before leaving, revealing how torn up he is. While it doesn't excuse his actions, it still stings to know how bad he feels.
Patrick's breakdown in Charlie's arms, right after the aforementioned fight.
Charlie's anguished call to Candace, where he flatly asks if he's responsible for his aunt's passing.
In the book, the poem 'To Santa Claus And Little Sisters' had this troper in tears for days
What Do You Mean, It's Not for Kids?: Because "family-friendly" actress Emma Watson appears here doesn't mean the film wasn't (briefly) rated R for "teen drug and alcohol use, and some sexual references" (it would be re-certified with a PG-13 certificate a few months before its release).