The test proving Keith really is Veronica's father.
Keith: You think that charm of yours is learned behavior? That's genetics, baby!
The part right before that, when she signs away her "inheritance" without a second's hesitation.
Before even that, when Veronica shreds the paternity test she sent (without reading the results) because she decided her capacity to be an heir to the Kane fortune was less important than keeping Keith as her dad.
Veronica confides in Wallace about her rape at Shelley Pomeroy's party and they hug emotionally.
Weevil hugging Veronica and genuinely thanking her when she gets him out of juvie.
Really throughout the whole episodem it's kind of sweet she's the only person looking to help him.
The end of One Angry Veronica, when Wallace returns and he and Veronica watch the ball drop for New Year's.
"It was worth getting taped to a pole. I'm gonna miss you."
More so because it seems to be part of the impetus for Veronica deciding to stay in Neptune.
"Dance with me." Though what really makes the scene a CMOH is the song lyrics.
The end of "Ruskie Business", where Veronica helps Meg find her secret admirer, aka Duncan. Verges on Tear Jerker because it is clearly hard for V, but she nevertheless thinks that Meg deserves it. And then it becomes a double heartwarming moment when you learn that Meg asked for Leo to come for Veronica.
From the same episode, Veronica helping Logan try to find out if his mom is still alive. When it seems like she really is dead, Logan breaks down in tears and Veronica holds him in her arms.
Wallace finds out who's been making him the spirit boxes that have been appearing in his locker all basketball season:
Wallace: I thought you didn't care about the whole school spirit thing.
Veronica: I don't. But you do.
And then when she's telling a player from a rival high school, "Wallace Fennel has a killer crossover. But it's really his sweetness and purity of spirit that makes him unbeatable."
When Veronica discovers her father's still alive at the end of "Not Pictured."
The moments where Wallace and Veronica discuss their best friend status in "Weapons of Class Destruction." It's obvious that Veronica's shocked to hear him call her his best friend and that it means a lot to her. Wallace's smile when she replies later in the episode that he's her best friend too proves it means a lot to him as well. Bonus heartwarming when you realize that it must be especially difficult for Veronica to admit she has a new best friend following Lilly's death.
The same episode has a flashback detailing why Veronica doesn't distrust The Dreaded student Clayton Norris. When Veronica had just become an outcast to the other student, some of those students spit at her with spitballs through their drink straws, and Norris responded by taking the straw from one of them and spitting in the student's face. He then smiled at Veronica, who smiled back.
At a memorial for Lilly, a video is shown that Logan put together. The Kanes clearly expected something stolid and dignified, but what they get is raw, unfiltered Lilly, full of life. Mrs. Kane is pissed, but Mr. Kane is overwhelmed with emotion, because it's the real thing in all her glory.
The hug where Logan comforts Dick and invites him to stay in "Welcome Wagon." Just remember that this is the "obligatory psychotic jackass" and, well, Dick. Proof of this show's excellent Character Development.
Dick apologizes to Mac for mistreating her when she was dating his brother. He plays it off as trying to hit on her but for at least a second you can tell he's sincere.
Wallace being ready to, ahem, "have a conversation" with Logan after he beats up Piz.
The fact that Logan only beat up Piz not out of jealousy, but because he thought Piz betrayed and hurt Veronica.
When Veronica and Logan are finding hookers for Max, because he fell in love with one at a nerd-con... when the right one shows up...
Max: Chelsea! "Chelsea": Oh my god, Max!? [meadow run moment] Logan: [goofy smile]
Veronica's aesop from Of Vice and Men
Veronica: So, what would Stan Marsh say in a situation like this? I think we all learned a valuable lesson about faith. You give it to the people you love. But the people who really deserve it are the ones who come through even when you don't love them enough.
I Am God. Veronica opens her acceptance letter from Stanford, and squeals with delight. Veronica hasn't been a normal teenager for a long time, and for a single moment, she gets to be.
In the final episode when Weevil finds out a sex tape of Veronica was released to a bunch of Hurst students, he drops his usual mocking attitude and tells her he's got her back. A few scenes later, it's shown that he put the car one of the guys who forwarded the video up on blocks at her request.
From the movie
Real Life example, but in March of 2013, Warner Bros. finally relented and allowed Rob Thomas to raise money for a Veronica Mars movie via Kickstarter. The condition was that they needed to raise at least $2 million in the span of 30 days (otherwise, the movie wasn't happening). The fans responded, donating $1 million to the cause in a span of four hours, and fulfilling the other $1 million in another 7 hours. 1 day down, 29 to go...
Ultimately, the fans broke the Kickstarter record of donators and exceeded even the upper level of the hopes that Rob Thomas had, getting over 5.7 million raised. "Not enough interest," huh?
In the first released promo, Weevil says to Veronica "Please don't make me look bad in front of my wife." Weevil got married! That and the way he's dressed seem to imply that Weevil really got his life together.
Nine years on, Veronica'a sex tape is still a big enough Berserk Button for Logan that he'll launch into a blind rage in defense of Veronica over it.
Wallace is the first one to jump in angrily to put a stop to it, which is fitting since it involves both his best friends.
The bad guy's got her cornered, with her only chance to get out is to time everything right, and she pauses to send a text to Keith, telling him she loves him. He's still in the hospital, and the last time they'd spoken, they were arguing over what she was doing with her life.
Veronica runs into her old principal, Mr. Clemmons, during the high school reunion. They trade snarks for a bit, and as they part ways, Mr. Clemmons stops her and tells her that it's been boring without her.
Seeing what Weevil's done with his life since Veronica left Neptune: quit the PCH, gotten married, had a beautiful daughter, and not gone near his motorcycle in three years. Especially the bit where he pulls out his cell phone to coo over his daughter with Veronica.