Tropes that apply to all four main characters (Captain, Sniper, Pilot, & Engineer):
Ambiguous Gender: This especially applies to the Captain. Sniper and Engineer were both eventually confirmed male, but the comic's creator continues to be deliberately vague about Captain and Pilot (although Pilot is now implied to also be male).
The Faceless: Only two of the main four have been seen without gas masks on, and even then their faces were always partially obscured by something else.
Gas Mask Longcoat: Only the Captain has the longcoat part of the equation, but they all have the gas mask.
Loving a Shadow: Thinks Captain to be a god, though Captain is implied to not reciprocate (responding with flat dismissal whenever Pilot makes advances through the blogs, and having said that his "minions" are "all equally tolerable").
No Name Given: A name is written on his jacket, but he doesn't think it's his. However, the Biomass calling him by it and his wearing the jacket in a pre-apocalypse flashback imply that it might be, and he is just too far gone to remember.
Subordinate Excuse: Definitely has a crush on the Captain. After Sniper gets swallowed by a whale, Pilot sends him a letter saying "Ha ha ha, now Captain and me can finally be together forever."
The Engineer (a.k.a. "Engie", a.k.a. Dr. Alexander Gromov)
Tropes:
Deadpan Snarker: When Captain's mug breaks and everyone freaks out, his only response is to raise his eyebrows, say "Well. That didn't sound good" and keep eating.
Foe Yay: ANNET called him "dear" and said "I love you" whilst trying to kill him years ago. In her recent return she referred to him as "my love", just before trying to kill him. Likewise, Engineer usually calls her "Annie", and before the apocalypse it was definitely a term of affection. He also has called her "my love." He even wrote a poem about her, in which he called her "my beloved".
Only Sane Man: Type 3. Unlike Snippy, he's completely given up/accepting and doesn't even bother protesting the strangeness of his companions.
Evolutionary Levels: The Cancer incorrectly refers to the Lifealope's shapeshifting ability as "evolving". In keeping with the trope, it seems to become more intelligent and complex with each shapeshift.
No Name Given: Unlike the other characters, it doesn't even have an In-Series Nickname. The closest thing is a wallpaper of it titled "WOLFALOPE." To compensate, fans have dubbed it "the Lifealope", a portmanteau of "life" (because of its Fertile Feet) and "wolfalope."
Shapeshifting: Started out as something resembling a salamander or lizard, then shapeshifted into a rabbit, then a fox/wolf-like creature, and then seemed to resemble a moose or deer before being killed by ANNET's ion cannon. It was reborn as a cat-like creature (a wallpaper by the creator calls it "CATALOPE"). The only features that have remained constant are its three eyes and the presence of antlers.