Before the battle against Alpha Kretin, Luigi asks Starlow to fight with Mario. Starlow promptly responds by smacking him into the boss himself.
While chasing Wisdurm, Luigi falls in a mucus pit. While Mario and Starlow are discussing how to proceed, he falls in again.
"Bowser keeps appearing like a rabbit from the ugly hat of a magician who stinks!"
From that same cutscene:
Fawful: You are a nuisance barge barging in at a critical time for us!
Bowser: Nuisance barge? GWAHAHAHA! Buddy, you're like a nuisance SUPERTANKER!
When Fawful forcibly extracts Peach from Bowser's body, the orb containing her form slowly drifts down toward Midbus... and suddenly darts over and deposits her on Fawful. Fawful is barely able to hold her and asks for help. Midbus ignores him and walks off.
Like other minions, once Bowser frees the Magikoopas, a short skit occurs. Though not as quick as the aforementioned goomba, some of the text gets a bit quick. (Magikoopas numbered according to on-screen placement.)
Magikoopa #9: We who are not worthy of the mighty Bowser's personal rescue must honor him...
Magikoopa #8: We, the Magikoopa corps, have attempted to find a suitable way to express our deep gratitude...
Magikoopa #5 (Jerry?): *turns right* And so we hereby present an invigorating and inspiring dance of utter joy and happiness...
Magikoopa #6: *turns right* No, wait. We talked this over, Jerry, remember? We were gonna sing a song of Bowser praise?
Bowser: Forget it, minions! Let's get a move on!
*Bowser turns around*
Magikoopa #7: ''*turns left* Just a sec. I thought we'd build a monument to his strength!
*Bowser starts walking out*
Magikoopa #4: *turns down-left to #7; Bowser stops after a couple steps* No, we were going to make his favorite food, right?
Magikoopa #11: *turns up-left to #6* Not me—I voted for polishing his horns with velvet shammies...
Magikoopa #2: We DECIDED this, remember? It was foot massage all the way!
Magikoopa #10: *turns up* I still think that taking lutes and singing praises is sweet...
Magikoopas: *turn to face Bowser again, jagged speech balloon, enlarged text* KOO-RAH!
The look on Bowser's face when Starlow refuses to find his safe combo until he asks nicely.
During the Junker boss fight, after sustaining enough damage, Junker goes up to Luigi and sucks him toward his vacuum hand, and throws him at the Trash Cans that accompany the Junker. Most of the time, he goes into one of the cans, where he must be rescued by Mario. On occasion, he doesn't go into a can at all, and bounces off of the rim.
The stupid little fist pump the Junker makes when Luigi lands in a can.
If Luigi is still in the trash cans after a bit he'll wave to Mario, and then the lid slams down on his fingers with him groaning.
How about the simple fact that Bowser's battle tutorial is Fawful observing his battle with Midbus, warning Midbus of Bowser's attacks and demanding Bowser not do certain action commands.
After Mario and Luigi beat the Bonus BossShroobs Mario quickly tells Starlow about them and how it was more or less Luigi (Baby Luigi to be more exact), who saved them all. She doesn't believe that at first and she actually asked how Luigi did it, "ferociously crying" - and she's dead-on right!
Bowser's reaction when he sees the train tracks through his secret vault (and the train tracks themselves). Made even funnier by what he says before going inside:
When Bowser literally burns off calories by sprinting on a treadmill. He then accidentally sets off a Bob-omb before reading the sign that says he's in a Bob-omb depot...not noticing the Bob-omb walking to a pile of boxes filled to the top with Bob-ombs. His reaction when it all dawns on him?
And the Bob-omb antics get an encore when he yells at his Bob-omb squad to quiet them down...and accidentally breathes fire on them setting off their fuse. His reaction just screamsOh Crap!
There's a hilarious reveal in a scene involving the green sock-like Sockops when Luigi is trying to save Mario from them. One of the Sockops has his name revealed. The name? Kuribo.
When you discover the Bob-Ombs in Bowser's Castle, you can choose not to free them and come back as the Mario Bros. If you talk to them, they'll try to attack you but realize they can't due to being locked up. Talk to them a second time and they'll tell each other to ignore Luigi.
Bob-Ombs: It's Mario! Get him! But how? Yeah Phil, how? We're stuck in a cage! It's Luigi! Ignore him! Ignore him!