Jason Nesmith's In-UniverseCreator Breakdown at the beginning of the film, to see a jovial, if not arrogant, star who at first seems to embrace the fandom in contrast to his least-enthusiastic co-stars, to have his positive outlook crumbled after listening to the gossip of two non-fans about the negative affects of the show's fandom and how it tainted the actors' careers, which sadly revealed to be not completely unfounded, and leads him to lash out at his fans and eventually succumb to alcoholism at his own home, as he watches old episodes of his show to pathetically try to find his comfort zone again. Jason was probably thinking "I Wish It Were Real" for his Galaxy Quest television fame to be really worthwhile and eventually becomes a Crowning Moment of Heartwarming and Crowning Moment of Awesome for him when he realizes how his show inspired an alien planet to turn it into a real experience, thus making him as giddy as child when his dreams comes true as he gladly embraces his television role for real.
Quellek's death always starts the waterworks. This innocent alien fanboy has considered serving Alexander Dane to be an honor, since he has followed the latter's character's culture and philosophy for his whole life. Alexander has to watch his fan diein his arms, and for the first time, he delivers his hated signature line with sincerity:
Quellek: You'll forgive my impertinence, sir, but even though we had never before met, I've always considered you as a father to me.
Jason explaining being forced to explain the true nature of Earth television and fiction to the naive Mathesar. It's like watching a slow, hard breakdown of a child discovering that there's no such thing as Santa (it even hits harder as Jason's actor played a Santa). He looks absolutely devastated.
Not to mention Mathesar's cheerful face as he tries desperately to hold on to his belief in the show, vainly attempting to counter Jason's statements about how the "ship" is actually only an inch long.
It's even painful how Jason finally manages to get through to Mathesar. As mentioned before, his species doesn't understand the concept of fiction and playing pretend (which is usually not malicious in intent) but through their interactions with creatures like Sarris they now understand the concept of lying. Jason tries to break it to him gently by saying that he's an actor and that they were merely pretending, but Mathesar doesn't understand, forcing Jason to use language the Thermian does understand: "We lied." Mathesar visibly flinches at the word as if he's been stabbed.
The entire scene when Sarris sneaks onto the bridge and starts killing everyone off. Even if you already know Jason's going to activate the Omega 13. It's still an amazingly horrific scene.
Both Jason's outburst at Brandon and ignoring him when they knock into each other and their communicators get mixed up can hit really hard for anyone who has looked forward to meeting a celebrity they admire, only to be severely disappointed, especially when coupled with the feeling that they somehow messed up.