Brooke hugging Peyton after Ellie's death and beckoning Lucas to join the hug despite Brooke's continued mistrust of Lucas & Peyton's feelings for one another after Lucas cheated on Brooke with Peyton the first time they were together.
Lucas and the river court guys going to Jimmy's funeral.
Episode 4x09, "Some Give You Away"
"The one I want next to me when all my dreams come true? It's you. It's you, Peyton."
Episode 4x20, "The Birth and Death of the Day"
Skills & Bevin's parents meeting for the first time, and for all of their worries about Bevin's parents not approving of Skills for his race, Bevin's parents tell her off... For not introducing them sooner.
Nathan being willing to give up his dreams of playing in the NBA & just get a job to provide for Haley & Jamie.
Whitey putting off retirement to take a job at a local college, so that he can offer Nathan a scholarship.
Nathan, Haley, Peyton, Brooke, Mouth, Skills, Bevin, Junk, Fergie & Chase all deciding to skip graduation if Lucas does.
Right at the end of the episode, Haley goes into labour in the middle of her valedictorian speech. After the episode cuts to black for the credits, the rest of the senior class starts cheering.
Episode 4x21, "All of a Sudden I Miss Everyone"
It's not really a typical example, but there's something heartwarming about the fact that Brooke's reaction to Mouth walking up to her and kissing her (just to do it since he'd always wanted to) is a laugh and a simple "okay." She doesn't yell at him, she doesn't react negatively in any way, she just acknowledges it, and it really does help her side of the Odd Friendship the two have.
Episode 5x02, "Racing Like A Pro"
Brooke & Peyton meeting Jamie for the first time since he was a baby.
"I'm glad you're my godmother."
Episode 5x12, "Hundred"
When Jamie asks if the day Nathan & Haley got married was his father's best day, he's told the day Nathan married Haley wasn't his best day, it was the day he graduated high school - Because that was the day Jamie was born.
Andy telling Lucas that as much as he loves Karen & Lily, he'd give it all up if it meant Keith was able to be with them.
Episode 6x04, "Bridge Over Troubled Water"
Haley & Brooke discussing Brooke's mother trying to take Clothes Over Bro's.
Haley: You okay?
Brooke: Yeah. I just wish I'd had a family like yours.
Episode 6x14: Lucas gives Jamie and Andre walkie talkies and says that when he was a kid he wished for a brother to play walkie talkies with. The episode ends with Nathan calling him on Jamie's walkie talkie and congratulating him on becoming a father.
Episode 6x19, "Letting Go"
Nathan & Lucas telling Jamie about Keith.
Episode 6x23, "Forever And Almost Always"
Pretty much the entire episode, due to it revolving around Lucas & Peyton getting married.
Episode 6x24, "Remember Me As A Time Of Day"
Karen returning to Tree Hill to meet her grandaughter.
Haley, Jamie & Mouth's reactions to Nathan making it to the NBA.
Whitey telling Dan that maybe the reason he's still alive is so he can achieve redemption.
Victoria telling Brooke to tell Julian how she feels, and Brooke finally admitting that she loves Julian.
Chase turning up in New York for Mia's signing, and the message she signs on the CD for him.
Episode 8x13, "The Other Half Of Me"
Brooke's father fails to turn up to his daughter's wedding, so when the time comes for the bride & groom to share a dance with their mother & father, Julian's father Paul swiftly steps in to dance with Brooke, noting "You're my daughter now."
In some strange way, the lengths Skills goes to in order to make sure that everything that could go wrong (And actually has gone wrong in past Tree Hill weddings) doesn't happen. It's paid off when Mia & Chase are found going at it in the back of the limo, and Skills tells the newlyweds that he had Julian's truck decorated on the off-chance something stopped them using the limo, and Julian tells him that he did a good job.
Episode 9x07, "Last Known Surroundings"
The airport scene, for obvious reasons and the ones that followednote despite it's length.
After Dan dies, Keith's spirit arrives to guide him into the afterlife & letting Dan know that he forgives him for murdering him, and he's proud of the man Dan became after that in his attempt to atone; topped off when Dan muses that he knows where Keith's going, but he probably won't be joining him, and Keith simply tells his younger brother that he's his "Plus One".
Haley telling Dan on his deathbed that when Lydia asks about her Grandpa Dan, they're only going to tell her about how much he loved his grandchildren.
Dan leaving Mouth $500,000 in his will, as a thank you for standing up for Nathan on the air in the midst of the allegations of him cheating on Haley & fathering a child, and Mouth subsequently using the money to set up the "Edwards Scott Memorial Scholarship" to help students who want to study anything to do with the non-playing side of sports.