Hello, Sailor!: The United States Marine Corps uses Navy chaplains, so he is necessarily this, although not in the usual form.
Memetic Molester: Invoked within the strip by characters. According to Uriarte, he's not based on any real-life person (Uriarte says the chaplains he knew were good guys), but that chaplains in general are Acceptable Targets.
Your Cheating Heart: Jody's a representation of the (fairly standard) fear of this happening to their beloved from deployed military personnel...but given the webcomic's intent is comedy, Terminal Lance plays this for laughs.
Black Bead Eyes: Boots are drawn this way to emphasize just how much they are subhumans.
Butt-Monkey: The point of Boot is to get fucked around because no one likes or respects him, be it forcing him into doing more work or just being a plain jerk to him because that's what happens to boots.
The Friend Nobody Likes: That Guy is literally the asshole who ruins everything for everyone. He kills puppies (and uploads the videos to YouTube), drives drunk, and does every obviously-stupid and/or distasteful thing imaginable. This results in all Marines being viewed as drunk Jerkasses, getting their weekend liberty passes cancelled over things they didn't do, and having to sit through hours upon hours of training about why they shouldn't do things they all know not to do and don't do anyway.