All There in the Manual: One page's update notes establish that the comic takes place around twenty years after the game. This is the information you need to understand why The Unreveal below is, well, an unreveal.
Bitter Sweet Ending: Possibly, Liam and Gadry are both dead, they never find out why the war was still going, Jeremy may never walk without a crutch again, and it is possible the ten escapees will just be replaced. On the other hand, there can only be eighteen people performing the war at once (nine classes each). By the end, ten of the current fighters escape, four are dead, and the Blu soldier is left alone with a Red Heavy, a Red Demoman, and a Red Soldier. It is possible that they kill the Blu Soldier and end the war before reinforcements come.
Boomerang Bigot: The BLU Scout spends most of the comic hurling gay slurs at the BLU Spy. He has a crush on the BLU Spy. Justified, however, as virulent homophobia is a phase some people have to pass through before facing up to the fact that they are in fact gay.
Break the Haughty: Rojo, first after being severely burned by the BLU Pyro and again when he fails to heal himself with the RED Medic's medigun, realizing he's going to be heavily scarred.
Cassandra Truth: "Well, it could be anyone, right? I could 'ave killed 'im." Luckily for Bleu, BLU Heavy thinks he's joking about accidentally killing BLU Medic.
Dangerously Genre Savvy: Bleu, of all people. When Rojo is on the ropes, he tries to push Bleu's buttons, namely, his fear of killing, to get him to turn on Scout and help him instead. Despite Rojo being exactly right about how much Bleu's recent kills bother him and how much he doesn't want to add another, Bleu doesn't take the bait and shoots him. He's willingly sacrificing his innocence, and for awhile, his sanity, because he knows the other choice will lead to even worse things.
Diabolus ex Machina: Red's death comes off as this (seriously, what a senseless waste of human life—which may have been the point, but still).
Heroic BSOD: Bleu when he realized that he killed BLU Medic and RED Pyro.
Hey You: The BLU Scout refuses to address the BLU Spy by anything but gay slurs. Even after he confesses his feelings towards the Spy. However, around page 136, when a certain sort of understanding has developed between them, he gives this up and calls him "Spy".
Hoist by His Own Petard: BLU Medic - He ended up receiving his own lethal injection, the one he intended for BLU Scout.
Homoerotic Subtext: Bleu and both Scouts (though there's far more with BLU Scout) which eventually crosses into text at the end. invoked
Limited Wardrobe: Justified, since the characters wear uniforms, complete with the classic Lampshade Hanging of opening the closet to reveal a row of identical clothes in page 111.. But sometimes the characters are seen in incomplete uniforms.
And as of the second to last page the Red Scout apparently becomes one for them, too. Yeah, he interrupts their first real kiss to tell them they need to get moving, but adds that they "can makes out on the bus", and is smiling quite happily while he says it.
Shoot the Dog: The first person Bleu kills on purpose is the RED Pyro, in order to save the BLU Pyro. The second person he kills is Rojo. Both times, he was rather shaken up that he just killed someone.
Shout Out: Several, throughout the comic, to some rather unexpected things. For instance:
pages 152 and 153 both contain subtle references to WarGames. (See the title of the comic and the handwritten list of passwords respectively.)
the title of this one is a reference to a Homestuck meme. (Read the comments on this one to see reactions from people posting in character as a number of the trolls, and at least two of the kids.)
The Unreveal: They never do learn any more about why the war is going on than the hints from the old RED Medic's logs and the old BLU Sniper's crazy notes. More blatantly, Bleu fails to access the computer in the abandoned building and thus never learns what it has to do with anything beyond "it has something to do with the trains and probably runs them automatically."