If you can return all 4 jewels quick enough to Booster during Marrymore, the kissing sequence shows Toadstool kissing Mario....and Booster and Bowser inexplicably kissing each other. One for the scrapbook indeed.
And then after you deplete the boss's health, Booster and his mooks come in and Booster just eats it. That's it.
If you come back and talk to Chef Torte after defeating Bundt, you find him working on another cake saying "Now ZEES cake vill stay put!"
Near the beginning of the game, Mario offers the people of the Mushroom Kingdom a summary of The Story So Far. Of course, since he's a mute protagonist, this involves acting out the events of the game to that point... which in turn involves physically transforming into some of the relevant characters, such as Princess Toadstool (as she was then still known in the West) and Bowser. When he transforms into Bowser, the Toads collectively jump back in shock, and some of them even hide behind the nearest available cover as if he were the genuine article. And when he re-enacts a long fall by disappearing off the top of the screen for a moment, one of the Toads runs over to the door and looks out as if to say "Mario? Now where did he go?"
Once Toadstool is rescued, the party explains the plot to the Mushroom Kingdom officials. A highlight is Mario portraying the giant sword Exor (complete with matching facial expression), while Bowser portrays his own castle. Ouch.
Mario's "Exor face" in general, whether he uses it to impersonate Exor or for other reasons.
If you stand on Frogfucius's table in Tadpole Pond and talk to him, he'll spout this little cookie fortune:
FROGFUCIUS: "Grasshopper, do you not think it rude to stand on my dining table?"
Gaz is a boy in Rose Town who idolizes his doll Geno, at the expense of other heroes. When Mario first enters his house/inn, he's pitting dolls of Mario and Bowser in battle against each other. Bowser wins (much to the obvious dismay of Mario, who is standing right there), so he can have his Geno doll defeat Bowser. Later on, when the now-possessed Geno tells Gaz that he's joining Mario on a quest, Gaz agrees that Mario needs all the help he can get. Mallow has to physically restrain Mario from decking the kid.
Right before this, in the scene after Mario and company defeat Bowyer, Geno reveals that he took his form because he thought that the puppet looked the strongest of all of Gaz's toys. Mario thinks nothing of it, but it's a good thing that Bowser wasn't around yet to get mad that Geno didn't possess the Bowser doll instead.
In the same town, there lives a gardener who seeks to have the legendary "Seed" and "Fertilizer", to make his plant grow. Each time that he's given one of the items, he gets overjoyed, to the point of running around frantically and talking really fast. The crowner is when said gardener reacts like this again after seeing his plant grow into a beanstalk. Needless to say, Mario gets bewildered reactions.
And after the seed grows into a beanstalk that reaches into the sky: "Do you think it might need a little more fertilizer?" Cue Face Palm from Mario.
One of Bowser's weapons, the "Hurly Gloves", comes with a Mario doll that is most likely intended to be thrown at the enemy. When Bowser uses it, he places it to the side and throws Mario instead.
What really makes it funny is Mario's surprised reaction and his arms flailing when Bowser does it.
Managing to get the Masher has Mario doing his victory pose with the line saying 'you got the masher' then the masher klongs him on the head causing him to collapse...ouch!
When Mario first appears in Nimbus Land, he arrives just in time for Valentina to pass Dodo off as the long lost Prince Mallow. The ruse is made difficult by the fact that Dodo gets stuck in the doorway on his way to appear before the townspeople.
After beating Valentina, Mallow obtains the key to free his parents. He then walks into the palace, Mario taps his foot for a second, then pulls out an umbrella. It then starts to rain.
Bowser is totally willing to ditch the party at the final dungeon since he's gotten his keep back, but relents when Geno explains that as long as Smithy is still active, he'll just send more troops through the portal over Bowser's Castle.
Bowser:(Quietly, to himself) More of these weapon-people barging into my keep? What about my..... privacy?
Upon encountering the Manager of Smithy's Factory, Bowser starts making his usual boastful threats, only to be completely ignored in favor of Mario. Once the battle is over, he takes a moment to reflect:
Like the moon over the day, my genius and brawn are lost on these fools. ~Haiku
You can inflict a long Work Off the Debt sequence on yourself if you overstay at the Marrymore hotel. Mario acting as a bellhop is hilarious enough on its own, made funnier by the owner's dialogue if you try to take a break, talk to him rather than helping guests, etc. And the former bellhop blocks your exit of the hotel until you pay it all off.
Just about everything Booster says and does. Highlights include eating Bundt (As mentioned above), tasting Toadstool's tears, and jumping randomly between thinking everything is a game and helping Mario out to deliberately hindering and attacking Mario.
Exor's face if you KO his mouth during the battle, made even funnier if you KO-d both of his eyes first. Also, the fact that his mouth is named "Neosquid" for no real reason.
This in itself is a translation error. In Japan, the mouth is called "Mouth".
On Star Hill you can read a lot of people's wishes. One of them is "I wish I wasn't such a crybaby." Mallow then berates you for not minding your own business.
Mario getting dizzy from jumping onto the head of and riding the hyperactive child in the Mushroom Kingdom who is constantly running around in circles.
The entire sub-story involving Booster and his attempt to marry Toadstool. As one L Per put it, imagine a stereotypical 4channer getting hitched.