"Eating this flower leads to spectacular, breathtaking indigestion."
Olimar finds the Paradoxical Enigma, a severed rubber duck's head, to be a stunning work of art. When he finds a more complete rubber duck in the Shower Room...
"The first time I laid eyes on this hideous treasure, I though it was a giant aquatic monster! It took me several terror-filled seconds to realize that it's just an ugly statue. What a relief... I was ready to run all the way back to Hocotate!"
It turns out Olimar likes karaoke, which his family apparently looks down on him for.
"Think back and remember the starry skies of your youth...Innocence...Every being once possessed it, but lost it over time. This star is the shape of that precious memory. All major credit cards accepted."
The second half of the battle against the Waterwraith.
The Pikmin going and beating up the Bulborb in the Good Ending of the first game.
The bonus video for completing challenge mode shows us some more detail about the reason for the plot. Louie was lying about the ravenous space bunny. He ate the entire shipment of golden pikpik carrots.
Some of the ship AI's reactions, especially after you make it store a deceased enemy, attempt to enter the Submerged Castle, and after it becomes gold plated.
Enemies falling off the side of the rusty metal stages. Especially if they're a Bulbear marching after your Pikmin so blindly that it walks out onto nothing and falls.
Plenty of the letters you recieve. Highlights include the President realizing he accidentally took a loan out with the All-Devouring Black Hole Loan Sharks, the President accidentally eating all the cookies that were for Louie, spam letters, and Olimar's family attending a performance and falling asleep during it.
In 2, the ship writes sales pitches for all the treasures found. Even the food.
"The consistency of the half-cooked yolk says "Mmm! Good!" It is packed with nutrients, too. I can sell it, but I have never eaten it. I am UNABLE to eat it. Not even a nibble."
Both notes on the Flare Cannon. The Ship says it should "never be used to cook sausages". Olimar says Louie keeps trying to use it to cook sausages.
In 3, all Pikmin can throw bomb rocks now. Those who do throw the bomb and run away screaming the Pikmin equivalent of "Run away!".
Charlie's odd fascination with his Rubber Ducky becomes an amusing Running Gag. It's especially funny when Louie runs off with it.
Between days in Pikmin 3, the crew mates can speak to each other. These random conversations can be quite funny.
Alph goes on about Charlie's legendary acts of heroism, such as "Operation: Rubber Ducky Stucky" and "Operation: Rubber Ducky up a tree".
Brittany tells Alph that she thinks that Pikpik carrots are gross.
After you save Charlie, his rubber ducky can be seen floating around aimlessly inside the ship, even floating past the map sometimes. When you capture Louie after he stole all your juice, he's tied up and does the same thing.
When the ship crashes at the beginning of the third game, you can hear the laugh of the Duck HuntDog.