Crazy Awesome: Don't give The Captain a reason to storm your base. Really, just don't.
Critical Research Failure: One of Captain's journals involves him/her comparing Snippy and Pilot to Pokémon. This is undermined by his/her complete misunderstanding of what pokerus does (it does makes Pokemon stronger, but has nothing to do with evolution).
His tumblr certainly doesn't do much to abate it, though the person who operates has said she will no longer be drawing OCs with Snippy on tumblr. Why? Case in point: "There are quite a few OCs who are... rather infatuated with Snippy, and as cute as that is, this is not the place for that."
The Captain and the Pilot enjoy giving each other piggy back rides and reenacting romantic scenes from Titanic (1997) together.
Captain to Snippy: "So, what are you wearing?"
It should be noted that there's no way of knowing if any of these examples really qualify as Ho Yay, since Zee Captain is Ambiguously Gendered throughout, and though Pilot, Engi and Snippy are revealed to be male, at first they are also ambiguous.
A few instances, despite the comic's humor. Among them are the... thing in the second panel of this strip, and the monster that inadvertently rescues Sniper and chases him across the city.
Sniper gets a big dose of this when he's embedded in the belly of a giant spider-beast, which is made up of other living bodies and skeletons, all embedded together in a scene out of Dante's Inferno. Oh, and the spider-beast screws with his mind as well.
Rewatch Bonus: Did you notice that the skeleton on the train in this strip looks suspiciously like the guy sitting on the train in this strip?? And did you manage to find the creator's name hidden here, here, here, here, and here? (Look really hard.) Did you happen to spot the Captain on the sign in the second-last panel of this strip, or notice that the girl in the first panel is carrying the cancer purse? Did you see the alien spaceship or the red deer (a form the Cancer uses at one point) in the last panel here? There's also a StupidFox poster-thing in the panel with the girl and cancer purse. In "Cancer's" attack, there's a crossover. To top it off, Vitaly himself has said about future plots, "If you're preparing to take a gamble at figuring out what's coming, you can find links to these plots in objects from older episodes."
The Woobie: Sniper. Bad things continuously happen to him, and his "only friend" is kind of a jerk. The fact that Word of God states he's actually a nice guy makes it even worse. His waking life was made difficult when the Good Directorate copyrighted sleep.
From the forum's character thread: "He's the intelligent, kind, yet highly unlucky character in the series. He questions the captain's motives, but still follows him, having no belief in anything else."
Iron Woobie: Snippy remains (probably) the Only Sane Man and a complete badass no matter how much crap the world throws at him.