Star Trek/Red Shirts:
During the episode, a kid in red shirt says: "Well I'm not going to sit here and wait to die like the rest of you!"
The kid in the red shirt makes a run for it, but is killed by the big scary monster. Star Trek had a reputation for killing off its extras, especially if they happened to be wearing red shirts.
The Red Shirts being killed was never more apparent than in Star Trek's "The Apple," an episode where 4 red shirts were killed within the first 10 minutes of the show. The kid in the red shirt has never been seen on South Park before (thus making him an extra), and he even had a Star Trek emblem on his shirt. In addition, this episode's title is a nod to the Star Trek episode of the same name.