Lindsay's character development in general; from grief-stricken and isolated to finally happy and off to follow The Grateful Dead.
Not to mention the scene in the final episode where she's dancing alone in her bedroom. It's one of the few times we see her genuinely happy.
Bill and Coach Fredericks bonding over an episode of Dallas. The look on Coach Fredericks' face when he realizes that Bill is trying to include him in something he cares about is oddly moving.
In "The Diary" Bill prank calls Coach Fredricks house and gets caught, but explains that he did it cause he was angry about always being picked last. Instead of The Coach being angry at the prank calls or scoffing at him he lets Bill (and Gordon Crisp) be the team captains for a day.
Also note that when Bill gets to pick teams, he immediately picks all the kids who are usually called last first.
Finally note the look on Coach Fredericks face when Bill actually manages to catch a fly ball from one of the jocks during the game. He seems actually pretty impressed and happy about it.
The Freaks showing up to Lindsay's math competition, and cheering inappropriately loudly from the back.
Lindsay putting on a costume and helping Jean pass out candy as per their Halloween tradition; especially significant after Jean's heartbreaking disappointment after Lindsay skipped out at the start of the night to hang out with the freaks.
Lindsey dancing with Eli at the end of the pilot.
Lindsay sneaking out of Millie's slumber party and telling her that she isn't the same person that she was last year, and can't go back to the mathletes seemed like it was going to be a big Tear Jerker scene, with Millie asking if she'll still be willing to play Uno sometimes together. Lindsay just says "Of course! Millie, we'll always be friends."
Any scene where the Geeks are hanging out with Maureen Sampson.
Ken asking Amy if she wants to kiss him in "The Garage Door"
Ken apologizing to Amy for revealing her secret in "The Little Things".
When the Weirs buy Sam an Atari at the end of "The Garage Door" because he's such a good kid, demonstrating that, no matter how weird they could be, they really loved and appreciated him. This moment is especially significant because Neal just discovered that his dad was cheating on his mother.
Millie comforting and taking care of an anxious Lindsay during her drug high in "Chokin' and Tokin'"
Any affectionate Lindsay/Sam moment, like the scene in the Weir's kitchen while Sam talks to Cindy on the phone in "Boyfriends and Girlfriends." For all the difference in their real-life ages, Linda Cardellini and John Francis Daley sold the brother/sister dynamic really well.
Bill inviting Alan to accompany him and the rest of the Geeks to Comic-Con after it's revealed that Alan's behavior towards the Geeks stems from anger at their refusal of his company in the lower grades despite them sharing similar interests.
Even though Alan turns the offer down, he acts a lot nicer to the Geeks, Bill especially.
Alan: Never thought I'd say this, but Haverchuck is the king.
After pulling the fire alarm to avoid failing a math test, being sentenced to the AV room as punishment, being mocked by Nick, a teacher, and an entire class for his inability to work a projector, and having his problems disregarded by Kim, Daniel is invited by the Geeks to a game of Dungeons and Dragons. Not only does he accept, he wins, and looks happier than he has looked all season, during the finale.
A small one for Mr Rosso: Usually his attempts at connecting with the kids are seen as dorky and/or trying too hard, but in "Carded and Discarded" he starts playing and singing Alice Cooper's "I'm Eighteen" in front of the five Freaks in his office. Ken, Lindsay and Kim seem mortified but at one point Daniel even sings along and Nick not only enthusiastically joins in but afterwards is thoroughly impressed by Mr Rosso.
Nick: Guys, Mr Rosso is really good at the guitar. Some of those chords are hard.
Of course its hilariously averted at the end of the episode, but even better, Nick's still rocking out to Mr Rosso.