After a hundred episodes Church takes a moment to reflect on how he's learned that it's wrong to hate people based on arbitrary political or military delineations. Instead you should strive to "despise people on a personal level." While not a great moral, it still rings true to an extent, in that one should not mindlessly hate because they were told to.
Church: You should hate someone because they're an asshole, or a pervert, or snob, or they're lazy, or arrogant or an idiot or know-it-all. Those are reasons to dislike somebody. You don't hate a person because someone told you to. You have to learn to despise people on a personal level. Not because they're Red, or because they're Blue, but because you know them, and you see them every single day, and you can't stand them because they're a complete and total fucking douchebag.
Captain Butch Flowers dying of an allergic reaction to some medication is this twofold; the first reason is that we find out this was Gamma torturing Church For the Evulz in Season 10, the second is due to Monty Oum's death by severe allergic reaction after surgery in 2015.
Caboose's cheerful shout of "Connecticut" is this when Tex and Wyoming meet each other again, now that we know that Connie was one of the few Freelancers Tex had any kind of emotional bond over, and whose death had the greatest impact on her of anyone.
Tex not showing any hesitation to kill Grif when asked to, once Season 15 reveals that it's not the first time she killed a sim trooper in orange armor with no remorse.
When the bomb inside Church is about to be activated, Tucker attempts to kill him in hopes of destroying the bomb. Church objects to that, not caring about the people around him in the slightest. This attitude comes to a change later. A sacrifice with an uncertain hope of success is exactly how he meets his end.
While threatening Andy, Tex emphasises how he will be just a memory after she detonates him. The ammount of irony is staggering seeing what becomes of Tex after Reconstruction.
Growing the Beard: It was during season three that the series slowly began to head towards a plot-driven structure with some moments of genuine Character Development. This was dialed down a bit in the fourth season, but soon returned in the middle and would stay that way for the rest of the arc's run.
Church's attempted Pre-Mortem One-Liner, after the reveal at the end of Reconstruction, considering he's partnered with Tex to take down O'Malley.
Church:I've got half a mind to kill you, and the other half agrees!
Also, Church's exasperated cry of, "Holy crap, who is running this army?!" becomes utterly hilarious when we find out the person running the Red and Blue armies is, in fact, Leonard Church.
In Season 4, Tex wonders that if she kills Church while he's a ghost, if he would "come back as a ghost of a ghost". That's essentially what happens in The Recollection. Church is killed in the finale of Reconstruction, and is revived in Recreation via Epsilon's memories of him.
Sheila's appreciation for her new Pelican-class dropship body is amusing when it turns out she's based off the AI FILSS.
Magnificent Bastard: Wyoming and Gamma cross into this of sorts during their story arc. Its unclear which one was the mastermind, but whoever it was managed to manipulate the team in order to get what they want. Though, they weren't successful, they did come close.
Never Live It Down: Caboose really only killed Church once with a tank (and that wasn't even entirely his fault). He sort of killed Church while the latter was possessing Sarge, but as a ghost form, he couldn't be killed, and Sarge got better. Yet, they won't stop giving Caboose crap about killing his own men. Though granted, this may be because this won't be the last time this happens.
Doc: Everyone! I have something to say! Tucker and I are in love, and we're leaving! Tucker: That's right! We're getting married and there's not a damn thing you can do about it! Not even you French-Speaking Lopez! Lopez: [Mister Tucker, you promised your love to me.]
Stoic Woobie: Later seasons reveal that Tex had been one of these the whole time. She knew EXACTLY the kind of torture that Church had been through, and was simply trying to watch over and protect the broken remnants of someone she had loved, and had demolished an entire military base trying to save.
Overlaps with Jerkass Woobie to an extent when you realise the reason she acts like a Jerkass to Church. Everytime she sees him, she's reminded of her failure and that the Alpha will never be what it once was. No wonder she can barely stand to be around him, especially after the Alpha Took a Level in Jerkass after the attempted breakout. Could also be Jerkass Fašade since she likely acted so cold to him in order to keep him distant or from becoming too attached to her, since it could, and did, lead to him discovering what he really was.
They Wasted a Perfectly Good Character: Grif's sister (Who's first name, Kaikana, isn't even mentioned in the show itself until Season 15) has barely any effect on the story, and disappears almost entirely after Season 5, despite all the fun gags or plot complications that could be built off his having a sibling on the other side.