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.
The Freaks showing up to Lindsay's math competition.
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.
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.