Jason: I decorated my gingerbread men in little "Star Trek" uniforms.
Paige: Good lord. Could you be a bigger geek? Why are they all wearing red shirts?
You have to know something about Star Trek to get the joke, garfield246.
It’s an old staple of the original Star Trek that secondary or extra characters in episodes (that is, extraneous members of the crew of the Enterprise) who were doomed to meet some sort of grisly end always wore red shirts. That’s how we knew who was going to bite the dust in the episode, and as a result, “red shirt” became kind of a shorthand way to refer to any doomed crew member in Star Trek.
The joke is that Jason’s Star Trek gingerbread men are all in red shirts because they’re all doomed to die by being eaten. In other words, it’s Jason’s warped sense of humor at work.