Mental Health
Charlie is introduced to us as a young man with lifelong mental health issues. From his early years he was plagued by clinical depression and has been traumatized by the death of his aunt when he was seven years old. It is assumed that his trauma surrounds his guilt about her death; she was driving to his house with a birthday gift for him when the accident happened. He is able to express his feelings of guilt, but not to explain or to resolve them, and is admitted to a mental health facility prior to entering high school.
Although he seems to have worked through his depression and is therefore deemed able to go to a mainstream high school. He suffers loneliness and bullying but is also able to make connections and friendships. Throughout the movie we see his mental health issues as something prioritized by his family and friends; they are not being hidden or glossed over, they are being addressed. In this way the movie shows the issue of teen mental health as important and public rather than something to be addressed in private or hidden. There is also a distinction drawn between teen angst and Charlie's clinical depression.
We learn later that his depression is a reaction to repressed memories and trauma resulting from sexual abuse by his aunt. This is another aspect of mental health that we are introduced to in the movie, showing that mental health is not one particular thing but a collection of events and experiences leading up to a diagnosis like depression. Although Charlie is the main character in the film there are also other characters whose mental health issues are also brought to the fore. In particular, his best friend had committed suicide the year before. This is not developed fully as a thematic or as a plot line but even alluding to teen suicide suggests that there is a spectrum of mental health issues that can afflict teens and their families.
Homosexuality and Prejudice
Patrick is gay, which is a fact he has never hidden, feels comfortable with and which he family are apparently aware of and perfectly happy about. However, because Brad is well aware that his father will not be nearly as open minded and accepting as Patrick's he is forced to keep their relationship a secret to avoid repercussions. Brad's fears are proved correct when his father hits him after discovering his son and his boyfriend having sex.
Brad's father is not the only character prejudiced against homosexuality; Brad's friends all bully and beat up Patrick, calling him a faggot. The theme shows how prejudice and ignorance can result in a kind of mob rule, and also sows that when people do not understand something they tend to attack it. Brad also attacks Patrick, desperate to show that he is not gay at all and that he rejects any suggestion of a relationship. Brad is intending to live his life as a straight person, even though he is gay, so that he can avoid prejudice and gain his father's acceptance, not understanding that he is allowing prejudice to affect him by changing the essence of himself.
Teen Drug Use
The theme of drug use comes up a couple times, seen through Charlie's first drug experiences. He accidentally eats some pot brownies and is both amusing and erudite afterwards, amusing his friends with his witty observations. A second experience, this time with LSD, has some less amusing and entertaining results. Although the subject is skirted around rather than actually addressed as a problem, it nonetheless comes up more than once and is seen as a contributor to Charlie's downward-spiraling mental health.
Sexual Abuse
The theme of sexual abuse is one of the main themes in the movie. Charlie's clinical depression and subsequent mental health issues were all triggered by abuse from his Aunt, and he has completely repressed this memory. It only resurfaces when Sam's touching him reminds him of the way in which his aunt touched him. The fact that he is a young boy abused by a female relative is an unusual way of dealing with the issue in a movie; more typically movies deal with abuse by male relatives. This stereotyping of abuse is also likely to be why Charlie's parents didn't realize that his aunt was abusing him; they simply weren't looking for it.
Although Charlie is the main character in the book and therefore the character whose abuse we concentrate on, Sam also tells him that her first kiss was from her father's boss at work who was abusing her at the time.