Signum delivering a Get a Hold of Yourself Man to Teana in the form of a punch that sends her flying back several feet. Signum's response to everyone worrying about Teana being cold-cocked like that:
Signum: "Don't worry, I held back."
From episode 15:
Vivio's epic faceplant, immediately after she was told to be careful when running.
Ginga's face after being told she'll be battling Nanoha, Fate, Vita, and Signum. Funnier because it takes a couple of seconds to sink in.
Mariel's delayed reaction to finding out Vivio's relation to Nanoha and Fate:
"Oh, so it's like she's their chi-WHAAA?"
Alto and Lucino Squee over Reinforce Zwei until she introduces herself and they react in horror as they learn she's not only cute, but also a few ranks above them.
Episode 12: The villains escaped, and managed to get their hands on the suitcase, and Vita is not happy with the situation. Just as she's giving her report, however, Teana and Subaru reveal that they "sort of did something to the Relic". Cue the villains arriving back at their base, and finding that all they managed to recover was an empty suitcase. The best part? It turns out Subaru and Teana transformed the artifact into a silly hair decoration and hid it under Caro's Nice Hat.
A minor bit from the conclusion of the fight between Fate and Scaglietti and his Numbers: Fate charges at Scaglietti and whams him with the broad side of Bardiche's Riot Zanber Calamity like with a baseball bat, sending him flying into a wall.
The scene from episode 13 when Hayate and Fate walk into the room where Nanoha and the forwards are trying to pacify a crying Vivio. Hayate comments rather playfully that "enemies" that the Ace of Aces cannot defeat do exist while Nanoha looks at her friends sheepishly for help.
In one of the earlier battles, Nanoha announces a training match - her vs. the still-fresh Forwards. Teana asks the others if they could dodge all of Nanoha's attacks, to which Subaru and Erio announce, without hesitation, that they won't.
In episode 16, Vita and Zest introduce each other during their battle:
Vita: "Time-Space Administration Bureau's Riot Force Six; Forward Stars' sub commander, Vita."
Zest Grangaitz: "Zest."
Before in the same episode, we see a shot where Erio, Caro and Vita are standing next to each other. They are about the same height; it's funny to see that Vita hasn't changed since A's and she won't.
In chapter 8 of the StrikerS manga, Nanoha confides to Hayate that she will have to keep an eye on her Forwards because "they get some really extreme ideas". Hayate's rebuttal of "kind of like you were when you were younger" followed by an image of Nanoha shouting "Maximum Power" with Raising Heart in her hands is very likely to make you laugh a bit.
In the same vein, in chapter 10 and 11 the Forwards and most of the Riot Force 6 personnel try to find out who is the strongest mage in Riot Force 6. Many amusing moments ensue.
After Teana asks Hayate if she could be the strongest one, due to her having the highest rank of "SS", Hayate replies, with a gleeful expression, that she is really weak and would lose to every forward with the exception of Caro. That is if Caro didn't use her dragons, leaving her with only buffing spells. And then she remembers that Caro got some combat training from Nanoha and worries that Caro too would probably be able to beat her. It's so awkward that Rein II is shown looking defeated and Teana sweat-drops at the revelation and her face clearly expresses a "what the heck is happening?" feeling.
A bit later Signum is asks who is it that she perceives as the strongest one. Shortly after that Signum remembers a mock battle she had with Nanoha, which she describes as "rather intense". Suffice to say, the one panel of that battle we are shown had Nanoha trying to fight Signum in melee with Raising Heart as a makeshift spear, with both Nanoha and Signum having expressions you'd expect from deranged battle maniacs who want to spill blood. It's both disturbing and worth a laugh.
The Establishing Series Moment is, of course, retelling the intro. It begins the same way, with Subaru telling us about the day Nanoha rescued her. But it ends with Subaru taking a very different kind of Hero Worship...
Subaru: That day I knew... I wanted to become that person's bride!
The series shows a funny deconstruction of animals using their mouths...
Vivio (wipes her face with a towel from Zafira): ... It has dog spit.
One example: Ginga begins working for Riot 6, but her entrance ends with her slipping on a banana peel and knocking out her father. Cue Hayate making her join due to her Cosplay Otaku Girl lusts needing a Dojikko like Ginga in.
Ginga slipping on a banana peel became a Running Gag in later panels, as everytime she is shown, there is a banana peel for her to step on.
Another one: After Reinforce wakes up and starts to eat dinner, Hayate and the Wolkenritter muse about how cute it is... including Signum. Cue the next panels wondering why the hell she was thinking that, ending with Hayate and Shamal gazing at her with a Slasher Smile and the subtitle "Ten years is plenty of time for brainwashing."