Dating What Daddy Hates: Ron's family are upset when they learn he's accepted a formal courtship with an anonymous party in Slytherin House. From the hints his suitor has dropped and the gifts he's received Ron guesses that his suitor is an older male pureblood of higher status.
Despair Event Horizon: At the beginning of the story, Harry was suffering so much at Privet Drive that he awoke the Horcrux.
Disproportionate Retribution: Voldemort hates muggles because he was picked on at the orphanage and they killed his baby snake. Voldemort tracked down his childhood tormenter years later and killed her child.
Enforced Cold War: Harry and Sirius after Harry reveals to Sirius that he's Dark. Sirius doesn't support the dark side but he won't betray his Godson.
Even Evil Has Standards: Tom is disgusted by Vernon Dursley. Also Original Character Lethfyren Malfoy, a Mind Healer of shady repute that Voldemort hires (and who Tom calls "a monster") will NOT "do kids." Voldemort himself is strongly against his followers abusing their children though he seemingly has no problems killing them, since he was quite happy to kill at least two children before the events of the story. But then Voldie has a soft spot in his cold black heart for wizarding children-not muggle children.
Everybody Knew Already: Harry, Tom, and Draco aren't as careful as they think. Ron, Blaise and perhaps half of Slytherin house knows that Harry is the Heir but have so far kept quiet.
Evil Mentor: While Tom plays The Corrupter for Harry, Harry acts as Tom's Morality Pet to the point that when they meet Voldemort both Tom and Voldemort are surprised by how much they've changed.
Exact Eavesdropping: This is how Ron learns what Dumbledore's plans for him are and how he learns Harry's secret about "Tom."
Fallen Prince: Draco gets a lot of crap for hanging out with the Boy-Who-Lived and a Weasley especially from his father.
Freudian Excuse: Harry's abuse at the hands of the Dursley's is most definitely NOT Played for Laughs. Also Draco is regularly tortured by his father with the cruciatus curse. And Tom had a psychotic break when the other kids at the orphanage killed his baby snake in front of him.
Girl Posse: One tormented the young Tom Riddle at the orphanage.
Good Thing You Can Heal: Vernon quickly learns that baby Harry heals very fast and so takes the opportunity to beat him even more.
Heel Realization: After Voldemort tasks Harry and Tom with running distraction duty at Hogwarts by setting the Basilisk loose on the student body they had originally picked the muggle-born Hermione Granger to be one of their first victims, but after a week of stalking Hermione, Harry and Tom realize how brilliant she is and decide to choose a different target. When Harry and Tom give their report at the next Death Eater meeting and explain why they switched targets this even get Voldemort thinking that maybe he was wrong about Muggle-borns.
Light Is Not Good: Dumbledore, Leader of the Light, has no problem with placing a child in an abusive household, using kids as pawns, or arranging for the deaths of his students.
Living With The Villain: Dark!Harry attends Hogwarts with the Light wizards and spies for Voldemort. It helps that no one wants to believe that the boy-who-lived could go dark.
Non-Lethal Warfare: Voldemort wants the Chamber of Secrets open but (on Tom's insistence that Harry not be forced to kill) Voldemort gives Harry strict orders to use the Basilisk to only petrify and not kill any students.
Parental Substitute: Tom for Harry. Tom essentially raised him and taught him how to survive and defend himself. Also Sirius for both Harry and Draco.
Progressively Prettier: Voldemort. After taking the philosopher's stone he's no longer a snake-face and he gets back his youth and Bishōnen good looks.
Roaring Rampage of Revenge: Tom Riddle's war against the muggle world really started when he was a child and a posse of muggle girls killed his snake.
Slash Fic: It's (pretty!)Voldemort/Snape and it will be Harry/Draco when they're older. Also Ron believes his secret admirer is male... and it's strongly implied that his admirer is Blaise.
Stalker Without A Crush: Harry and Tom for Hermione. They begin stalking her to learn her schedule so they can sic the basilisk on her but soon become intrigued with her instead.
Stalking Is Love: After receiving gifts from his anonymous suitor Ron feels comforted that at least someone out there likes him.
Start of Darkness: Tom's is the bullying he endured at the orphanage and the final straw is when they killed his pet snake, Harry's is the horrific abuse he suffered at the hands of the Dursleys.
Stockholm Syndrome: From the offset Tom is completely honest that he killed Harry's real parents. He still becomes Harry's father figure and Only Friend.
Training from Hell: Harry when Tom is teaching him magic. Later subverted, Lucius claims that he tortures Draco in order to make him strong and teach him how to be a man. Draco eventually comes to realize that Harry was right—his father does not really have his best interests at heart and is just hurting him for the sake of hurting him.
Transparent Closet: Draco is the trio's resident expert on clothes. Also Harry and Draco share an awkward bro-hug.