Ass Pull: Most of the second half of Episode 10. ThornBrain admitted that he "made it up as he went along". Subverted when Episodes 1-3 were remade shortly after, wherein they made sure to foreshadow it. See the Chekhov's Gag entry for what in the episode was planned ahead.
Giroro. Flashbacks makes him nauseous, and he is allergic to cats. Episode 17 also revealed that he never properly learned how to shoot a gun and never finished military training, evidenced by his failure to land a single shot on Garuru.
Invoked with Zoruru, and after only one scene. His first appearance has him kill Koyuki immediately following a Pre-Mortem One-Liner. His second appearance has him getting a disruptive Skype call from his mom, followed by excessive paranoia about how Natsumi must want to start dating him.
Todd Sirkowski of Todd's Toilets flying by in a hot air balloon and immediately crashing/exploding. Three times. Eventually subverted when Aki shows up and hints that this thing has happened before.
Mint's Hints from Episode 8, the Keroro Platoon's "animation" consisting of a single badly-drawn frame and Mario Paint music, was one until Tororo brought it back for Episode 17.
Keroro's delirious engagement of "Keroro Love Fighters" in Episode 15. Despite apparently flinging himself across the room and terrorizing his friends, they never bring it up again.
Continuity Lock-Out: Every new episode's plot and several of its jokes are closely connected to the events and jokes of previous episodes. The team has noted that new viewers often start with the most recent episode, leaving out 2+ seasons' worth of jokes and continuity. The channel description requests that new viewers start from Episode 1, and a clip reel was made to serve as an introduction for those not interested in doing so.
Crosses the Line Twice: The games Keroro and Giroro played with Zeroro: "Zeroro Dies", "Zeroro Plays Chicken With a Bullet Train", "Zeroro Hides-and-We-Take-His-Stuff-Seek".
Dororo was this at the start of the series. Yoshi didn't even want him in the series before his first appearance, but he became the one character who developed the most over time.
Tororo got a massive wave of praise after Episode 17. It could have been because Tororo has a large fanbase already, or simply because Travis did that good a job.
Practically every non-recurring character became one, including Asami, Grandpa Viper, the animators, Joriri, Pururu, and the "teeth guys". Yoshi often lamented that these characters did not show up more often, since he loved how they came out. Thorn and Jacob were particularly happy to bring Pururu back for Episode 25, and she ended up being Jacob's favourite to write for.
Kululu for Thorn in Season 3. Thorn didn't like Kululu much for most of the series, but for Season 3, since Kululu no longer cared about what was happening and didn't seem to do anything of purpose, Thorn and his co-writers were able to do ridiculous things with him. "Pineapple boats" alone made him one of Thorn's favourite characters for that season.
In Episode 15 Fuyuki randomly says he no longer believes in God. The line, though otherwise unconnected, was written around the time of Christopher Hitchens' death.
Saburo's original voice actor DFatman intended to voice him as a drunk. When Fatman was kicked out of the team, Thorn and Yoshi decided to leave Saburo mute for Rule of Funny, until Episode 18 when he was very briefly voiced by MrFailGame... who later died from alcohol-related problems.
Hilarious in Hindsight: The writers made all of the characters defaulted to bisexual unless stated otherwise, and Giroro was also made a Wholesome Crossdresser. Writer ThornBrain came out during production of Episode 11 as a bisexual transvestite, which he was only starting to realize around the time Giroro was made a crossdresser.
The series made Keroro and Tamama a couple. Subverted after Episode 10, when it is discovered that Tamama is actually a girl.
Giroro and Dororo. Dororo actually hit on Giroro at the end of Episode 6, they have a semi-serious bit of bonding at the end of Episode 7, and they are noticeably closer friends by Episode 11. Then in the Post-Credits to Episode 14, Dororo asks Giroro to marry him. And then They Do get married in Episode 15. Giroro even says "We've been fucking behind your backs for months!"
Growing the Beard: Thorn and Yoshi consider Episode 4 to be the point where everything in terms of writing and voicing started to gel, be it due to the expulsion of previous redundant team members or simply the introduction of Dororo. Yoshi also didn't pick up as a voice-actor until Episode 4, nor did he enjoy voice acting until then. After Episode 18 Yoshi said he considers it a favorite, especially when Dororo shows up.
Bringing Travis in to help write Episode 9 was Thorn attempting to prevent this trope after a particularly idea-less Episode 8. Episode 10 was also written with a back-to-basics approach after Thorn realized that Episodes 8 and 9's biggest flaw was that they were too self-aware.
Writer Thorn considers Episode 13 to be the series' low-point, and although the episodes after were fine, he thinks Episode 17 was when SFA finally dug back out of it and truly get its spark back. This was mainly due to him and Yoshi jumping ahead and planning for 17, and the resulting excitement for such a later episode left them with no ideas or motivation for 13. It took them three tries to find an episode they could work with, and the resulting script was dry and unimpressive. Yoshi and Travis generally agree that 13 was "kinda bad", whereas all three (and many viewers) agree that 17 was one of the series' best episodes.
Tear Jerker: Fuyuki's speech to a brainwashed Keroro in the finale:
Fuyuki: "You're right, Keroro. It is funny. Somehow you managed to turn everything that happened into everyone else's fault. You ever think about why you can't make people happy? Because nothing you've done in your entire life has been for anyone else. You hurt my sister for questioning you, you abandon Tamama for being herself, you take advantage of Giroro for keeping the team together, you mock Dororo for his undying devotion to you... and tell me, Keroro... Did you ever once think of what I go through to protect you!? (Crying) You donít care about anyone... You just drag everyone through the dirt... Now everyone who ever cared about you hates you... But it didn't matter to me. You were my friend, the only real friend I ever had. I took everything you gave us... ícause I wanted you to be happy. Does that mean a fucking thing to you?!"
Viewer Gender Confusion: Even Tamama didn't know she was a girl. This came about as a result of Writer Gender Confusion: for the first several months of the team's existence, Thorn kept thinking Tamama was a girl. By Episode 3, he and Yoshi just decided to make it that way.