Episode 15, where Church and Sarge meet in the afterworld, a monochrome version of Blood Gulch, which doesn't make any sense considering that Church was never dead. This is subverted by a retcon seven years later: Revelation shows that he was just in a recovery mode activated when soldiers are incapacitated.
Episode 28.5, "The Last Episode Ever". It first aired on April Fools Day.
Episode 45.9, "The Greatest Episode EVER". An episode made entirely with paper cutouts by Gus Sorola while the rest of Rooster Teeth was out of town.
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.
"Funny Aneurysm" Moment: 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.
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.
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.
Moral Event Horizon: Sarge crossed this line in the season 5 finale. Granted, he's technically saving the day, but his tone implies that he actually does what he does out of spite and anti-blue sentiment rather than a desire to thwart Omega's plan. In fact, he might not even be aware that there was an Evil Plan for him to thwart. That said, people seem to forgive him, or at least let him off the hook, by the next meeting of the teams.
In one of the alternate endings (see "Fight! Fight!"), Church and Tucker certainly think so. Though that ending also has Sarge being a dick and really rubbing the whole thing in to a degree he never did in the other endings.
Never Live It Down: Caboose really only killed Church once with a tank (and that was due to it malfunctioning because of Church). 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 developing too attached to her, since it could, and did, lead to him discovering what he really was.