- The player is first introduced to Shepherd babbling in fear as she clings to a wall to avoid some Bulborb Larvae, who can still be taken out with one punch. Not exactly the best of first impressions, is it?
- Encountering Red Pikmin for the first time has the Pikmin take interest in Oatchi, by chasing the poor dog around in circles for the rest of the cutscene. And all the while, Shepherd is cowering in fear of the Red Pikmin behind Collin.
- The Groovy Long Legs will occasionally blast you with an airhorn that sounds like it was ripped straight from an MLG montage. It also gets in one last airhorn before it explodes on defeat.
- Really, the entire concept of Groovy Long Legs is this. It's a sentient disco ball that stomps to the beat of its own music, enters the battle by performing a headspin like a breakdancer, and can even trip up and leave itself vulnerable, complete with a goofy rendition of the Pikmin theme.
- For those playing a Night Expedition for the first time, seeing the Onion rev up along with the S.S. Beagle might have you think the Pikmin are coming with you. Nope! The Onion continues straight up into the atmosphere as per normal. The Pikmin might be loyal, but they're not that brave — and for good reason.
- If you fail a Night Expedition, Dingo will offer his help because Shepherd tells him to. Should you accept, there's a fade to black as Dingo goes full ham on the rabid enemies with a cacophony of cartoon sound effects and his muttering giving away his true thoughts of the situation. As it turns out in the debriefing, Dingo won because he used a ton of Bomb Rocks to kill all the creatures, Yonny mentioning that the Glow Pikmin didn't even notice he was there as a result. Dingo still insists that he completed the objective.
- At one point after a day, while discussing the use of the Charging Horn, Russ reveals that it also has a function to make anyone charge, including people as Russ soon demonstrates. He explains he was demonstrating how to use it in case of emergencies, only for Shepherd to vow to make sure that "emergency" never occurs.
- After getting harassed by the Waterwraith in the Engulfed Castle cave, the final area is a perfect replica of its hilarious defeat from 2: Finding Purple Pikmin Candypop flowers and using the newly-acquired Purple Pikmin squashing it to oblivion while it panics and eventually flails away after its rollers get smashed. To cap it off, you get a Nintendo Gamecube disc (of Wave Race instead of Pikmin 2, sadly) and a tube of purple paint buried nearby, as if the devs were saying "Yes, this is how powerful they are" or to returning players combined with the game disc: "Yes, they're just as busted as before."
- The Waterwraith actually isn't completely defenseless in its second phase — if it flails into you, it'll knock you clean off of Oatchi with a cartoonish sound effect, scattering your Pikmin everywhere. It's hard not to get a laugh out of it when it happens.
- Even later in the game, the game pits you against two Waterwraiths… in a cave that recommends Purple Pikmin. They'll never stand a chance.
- How can you stop the well-meaning Moss from abducting your Pikmin and potentially leading them into danger? By tossing a Pikpik carrot at her, which she'll proceed to bark at for a long period of time before she realizes it's not actually a Pikmin.
- If you aren't riding Oatchi while exploring the Hero's Hideaway, he'll occasionally wander off to bark at Moss, as dogs are known to do when meeting other dogs in real life. If you don't have any Pikmin with you, Moss might return the favor and bark back.
- The Memory Fragment series of treasures are a bunch of puzzle pieces, with their names noting what part of the puzzle they might be (like the corner and edge pieces). The names get a bit unsure of where certain pieces belong, however, labeling some as "Bottom-ish", or just giving up and going "Bottom...Probably?"
- The Breadbugs are back and now goofier than ever. If you manage to whack one with a Pikmin and deal damage, the Breadbug will stop whatever it is doing to run around in circles whilst making hilariously pathetic panicked squeaks. The Giant Breadbugs, on the other hand, don't get scared; when they get hurt, they get mad. Do damage and the Giant Breadbug will throw a short temper tantrum before attempting to ram into you. (It should be noted this ram is completely harmless.)
- Olimar's Shipwreck Tale, being a shortened version of Pikmin (2001), has less unique parts. Most of them are Automatic Gears or Extraordinary Bolts with the rarer Repair-Type Bolts thrown in, but there are still specific parts for reconstructing the Dolphin or collecting for Olimar's peace of mind — such as the Omega Stabilizer, two Ionium Jets, Libra and Sagittarius, and Secret Safe, among others. One part which got this treatment? The Pilot's Seat. Olimar still refuses to leave without his favorite cushion.
- There's also all of those Extraordinary Bolts. If you remember in the first game, Olimar bought one because the salesman told him it had an "extraordinary" quality undiscernable to the average eye, with the clear implication the thing is actually worthless. (Or maybe not, due to it being a required treasure.) It seems that in this timeline, the sales pitch was so effective he bought several more.
- After rescuing Olimar and speaking to him at the base, he'll reward you by teaching Oatchi Moss' "Swallow" technique once the pup can carry 100 weight, which allows him to compactly carry most large things solo in his mouth, including things ten times his size like watermelons.
- The Piklopedia is back and it's still a great source of laughs as always and while you get Olimar's usual scientific notes and lore about the wildlife after rescuing him, Dalmo's notes only gush over how cute the creatures are and/or the ingenuity of their instincts. Louie's are of course, the best way to eat them.
- When you first unlock Louie's notes, Dalmo comments how Louie's notes are shocking but he supposes it's a unique way of showing love to creatures.
- If you feed any of the adult Wollyhop enemies Pikpik carrots, it can lead to some situations where if the wollyhops get too close while performing their Ground Pound, it can result in one wollyhop crushing and killing the other one as it grazes its victim's face, leading to some hilarious interpretations. It has to be seen to be believed.
- If you feed a Red Bulborb a bomb rock, the look on its face is absolutely hysterical as soon as it realizes what it just swallowed.
- Louie's notes on the Ancient Sirehound and Moss, rather than describing how to cook them (as that's a bit too far even for him), are reviewed as if they were cars. He praises Moss for being "Compact, with a tight turning radius", and calls the Ancient Sirehound "the ultimate ride, plush and comfortable".
- Concerning the Pikmin, Louie notes that Red Pikmin look like they taste good but he's "practicing restraint". He also feels the urge to put his hand in a Blue Pikmin's "mouth" just to see what would happen, may have once broken a tooth on a Rock Pikmin, and notes that the Glow Pikmin "doesn't smell alive."
- Louie's notes on how to cook enemies are usually quite detailed, but his entry on the Sunsquish, which looks like an egg yolk, just says, "Season with salt and pepper."
- Louie's entries in the Treasure Catalog are fairly short but priceless, detailing him eating or just goofing off with the inedible items, provided he didn't consider the possibility of them being edible.
- He seems to find the Rubber Cutie series tasty-looking, and considers the smallest variety "the right portion size for me". Perhaps now we know why he decided to steal Captain Charlie's rubber ducky in addition to all that juice...
- His only comment on the S.S. Peppermint is that it's "a strange way to serve toothpaste".
- He thought the Wind Detector (a harmonica) was a chocolate bar until he tried to bite into it.
- The Back-at-the-Beginning Track includes the anecdote that he got his head stuck in one of the gaps at one point.
- His notes for the Mega Horn read that he wants to try and scare his boss with it.
- He treats the Leisure Car like a thrive-thru window, complete with critique on its service speed.
"Place your order on the right, and pick it up at the left window. Beware- service is slow."
- Louie's notes on the Subterranean Swarm have him note that he likes how sticky the place is. We already knew Louie was an oddball, but this is something weird to stay even by his standards.
- On occasion, the Pikmin will sing collectively… and one of the songs they can choose from is a shortened version of the Waterwraith chase theme from Pikmin 2. Really highlights how cheeky the development team can be.
- Olimar praises his own taste in music in the description of the Harmonic Synthesizer treasure, but it turns out he's not very good at singing, as both his family and – in another of his logsnote – the Pikmin themselves do not like his attempts at singing. In particular, the Pikmin went completely silent at him attempting to join in.
- The double Waterwraith battle in Cavern for a King has a funny moment occur if you destroy one wraith's rollers. If the vulnerable Waterwraith runs into the other one, it'll crouch down and let the other Waterwraith roll right over it. Surprisingly polite for an Eldritch Abomination.
- During the otherwise tense fight against the Ancient Sirehound, there is something very comical about grabbing its tail with Pikmin, causing it to look over to what's going on there and trying to reach over as if trying to bite at its own tail, only to end up leaning too far and land on its back. Despite its intimidating appearance, the worried face it makes as it reaches for its tail and then flops over makes the giant dog look kinda pitiful and oddly cute.
- The fact that the Sirehound can fly. The image can be quite amusing. Well, not so much the part where it can send out puddles of Gloom and send your Pikmin and Oatchi into a panic, but it wraps right back to funny again when grabbing its tail in this phase causes it to panic and still flop onto its back.
- One extra funny bit is that with Louie on the Sirehound's back, he ends up right under it whenever it flops, giving the hilarious image of him being squished whenever this happens. Considering all the trouble Louie puts everyone else through, it makes for greatly comical karma. And considering how often you'll be flipping the Sirehound throughout the fightnote , it handily explains why Louie isn't able to muster up any more resistance after the fight.
- With much of the game's soundtrack being light and airy ambient music for the most part, it's pretty dang amusing to hear something as outrageous as heavy metal music serve as the Sirehound's boss theme.
- The fact that the Sirehound can fly. The image can be quite amusing. Well, not so much the part where it can send out puddles of Gloom and send your Pikmin and Oatchi into a panic, but it wraps right back to funny again when grabbing its tail in this phase causes it to panic and still flop onto its back.
- The ending shows the Ancient Sirehound, now free of Louie's influence, happily living alongside Moss and the Pikmin. Doubles as a Heartwarming Moment too.
- A bit of Fridge Humor too, when you consider that due to the captains' tiny sizes, the relatively colossal Sirehound is actually about the size of a real-life lap dog.
- The way you rescue Leaflings running Dandori Challenges. You work so fast that they get dizzy just from looking at you and pass out, allowing you to carry them back to the S.S. Beagle.
- The Civilian I.D. for Horatio bluntly states that he thinks he's someone who spreads cheer wherever he goes, when usually it's the opposite. Collin lampshades that it's a pretty blunt thing to say on your own I.D. card.
- If you talk to Yorke enough, then he'll mention that Don Bergman occasionally tells stories about his time as a space ranger. Yorke mentions that Don Bergman used to have a partner that he called "Ducky", the two either best friends or butting heads depending on the day. Considering he also mentions Koppai headed towards a food crisis, it's not hard to guess who.
- The face Moss makes when she spots a Pikmin. If you ram into her enough times, she will do a goofy waddle, all while making another funny face.
