Nathan making a free throw without even looking, showing up Damien West. There's a reason this would go on to be in the opening titles from the following season, and again when the opening titles were brought back in Season 8 . And be used as the "High School!Nathan" shot during the final scenes of the series.
Episode 4x09, "Some Give You Away"
Nathan, Lucas & Skills leading the Tree Hill Ravens to their first State Championship in the history of the team. Bonus points for being Whitey's last game as Coach, and the last game of basketball Lucas will ever play due to his HCM.
Episode 4x16, "You Call It Madness, But I Call It Love"
Brooke and Peyton both teaming up to beat the crap out of Psycho!Derek after he kidnapped Peyton.
Episode 4x21, "All Of A Sudden I Miss Everyone"
Mouth punching out the guy harrassing Shelley.
Jerk: I was gonna take it easy—
[Mouth floors the guy with one punch]
Mouth: Yeah, me too.
Later, he jumps off the roof, marches straight towards Brooke, and kisses her because he's "always wanted to do that" and walks away.
Episode 5x11, "You're Gonna Need Someone On Your Side"
Brooke finally standing up to Victoria & firing her from Clothes Over Bro's.
Episode 5x12, "Hundred"
Dan rescuing Jamie from Nanny Carrie after she kidnaps him at Lucas & Lindsey's wedding, giving her one hell of a pants-wetting threat in the process.
Dan: My name is Dan Scott, I think you know my grandson. Itís okay, you can blink once for yes. Thatís what I thought. Well, youíre done knowing him for the rest of time. And if you forget, or if you decide to go anywhere near my family again, letís just say this - I killed my brother in cold blood, Iíd have no trouble killing you.
Episode 6x05, "You've Dug Your Own Grave, Now Lie In It"
Deb taking out Carrie as she chases Haley & Jamie out of a cornfield; swiftly followed by Dan shooting Carrie as she gets up with an axe in hand, unbeknownst to Haley & Deb.
Deb: I guess there's a new crazy nanny in this town, bitch.
Episode 6x13, "Things A Mama Don't Know"
Brooke beating up Xavier after he attacked her at the Clothes Over Bros. store.
Episode 6x19, "Letting Go"
Rimkus being called out her incompetancy as a teacher by Jack & Sam.
Rimkus: Congratulations. You've set a new record for failing.
Jack: We didn't fail, you failed. Bring back Mrs Scott.
Sam: He's got a point. Maybe we wouldn't be failing if you hadn't fired our teacher.
Rimkus: Watch it, or you'll be joining your friend, Mr No-Name.
Sam: All I'm saying is, that either we all got instantly dumber, or you should've been a little bit smarter. I'll see myself out.
Haley's English class walking out of school, and heading to the Scott house to get Haley to teach them, since Rimkus is a crappy teacher & they aren't learning anything from her.
Episode 7x07, "I And Love And You"
Dan using a lie detector test to prove that Nathan didn't cheat on Haley & get Renee pregnant.
Episode 8x11, "Darkness On The Edge Of Town"
The entire Quinn/Katie fight, full stop.
Episode 8x20, "The Man Who Sailed Around The World"
Clay, Julian & Nathan confronting Ian Kellerman after they find out that he was the one driving the car that ran Brooke & Jamie off the side of the bridge before leaving them for dead during the storm.
Episode 9x03, "Love The Way You Lie"
Haley stands up for Dan. Yes, you read that right.
Episode 9x06, "Catastrophe And The Cure"
Dan effortlessly destroying the motive the Tree Hill police had for him being the one to kidnap Nathan.
Jamie standing up to Dan & demanding to know what he's done with his father. Remember that Jamie's only around 9 years old.
Episode 9x08, "A Rush Of Blood To The Head"
Chase beating the crap out of Chuck's abusive father.
Episode 9x10, "Hardcore Will Never Die, But You Will"
Nathan gets a minor one, as when Dan realises that he's out of shotgun shells & switches to his sidearm, Nathan picks the shotgun up again. When Dan tells Nathan to leave it since he's out of ammo for it, Nathan points out that the kidnappers don't know that.
Julian playing the role of Big Damn Hero by hitting the shady cop over the head whilst he has a gun a pointed at Nathan. Especially considering Dan had specifically told him to leave, so that there would be no risk of Brooke having to raise Jude & Davis on her own.
After a smarmy record exec smugly tells Chris Keller that her label isn't interested in signing any acts that sing about breakfast foods, just rock acts, Chris simply tells the house band to play "Blues riff, F-sharp minor" & promptly rocks Tric with a performance of "Loaded Gun".