Smoldergeist's constant threats about how you'll never make it past the Tutorial Level, and his constant surprise/annoyed response when you succeed. But one piece of dialogue even reveals Peach of all people, who you're chasing after, is easily getting past them too!
Smoldergeist: "And right after the pink one won as well... this test stinks."
During the boss fight against Smoldergeist, Starlow comments that it might get too hot with the purple fireballs against the brothers...so she casts a random gust of wind out of nowhere. The Bros. just stare at her, possibly wondering how she could do that.
After Brickle gets stuck in the fountain machine, the nearby tourists are unimpressed that the machine is broken with his presence. The tour guides then make up some incredible facts to amaze them. It works.
Nearby, there's a Yoshi who wants to taste a fruit, but he can't do it because there's a Brock staring him from afar.
Boss Brickle trying to catch the rabbit in Dreamy Mushrise Park:
Brickle(In carrot suit): Mm-MMM! Nummers! Ain't DAT tasty!
At the first badge shop they come across, the bros. are offered two badges for 1000 coins, but they seem to refuse the "deal." The Brock then starts to reduce the price, only for each of them to reply with "oh" and "hmm" as if thinking that the price is too damn high. It gets more and more ridiculous once the Brock desperately reduces the price to single digits until he gives up and gives them for free, which then he complains that he needs to work on his haggling skills.
It's really impressive that Mario and Luigi felt that 1 coin was too expensive.
They try to do the same thing later on as a hermit offers the Mario Bros a mini-game (for a price), but it fails.
During their quest to find Big Massif, the tour guide inside the dream world suggests the brothers to take the "Mushroom Deep Dive" tour. Luigi looks giddy and wants to try it out until Mario stares back at him and makes him say no.
When they do find Big Massif, his disciples try to show the brothers how strong he is. After some rock-breaking, they toss a huge boulder his way that is completely out of his league. He tries to destroy it with his head but he gets squashed underneath...then he pops back up behind the brothers. The disciples take this as a surprise opening attack from him, which he clearly didn't think about doing.
Later on, the group reaches the summit of Mount Pajamaja. The entire exchange is amazing.
Big Massif: BEEF!
Lil' Massif: FOR!
Big Massif: TWO!
Both Massifs: BEEF STEW!
Luigi trying to cheer up one of Big Massif's dream disciples (Sorrow Fist) to do better. Only at the end then Luigi realizes he's agreeing to his opponent saying that he will crush them.
Drinking from the fountain on Mount Pajamaja makes Mario and Luigi fall into a deep (and very trippy) sleep, during which they apparently find a giant pile of mushrooms, consume to their hearts' content, grow huge, and then are unable to return to normal. A GAME OVER screen appears, and after a moment Prince Dreambert wakes them up.
There's also a trippy fountain in the Dream World version of Mount Pajamaja though the dream appears to have a happier ending. It's still Fission Mailed though.
During their Dream Egg hunts, the bros. have to talk to these quirky seahorse siblings to get their eggs:
The first one is convinced that Mario, Luigi, and Dreambert are part of his favorite anime show, and the trio tries to impress him with poses and quotes. At the end of the day, the seahorse exclaims that it's just painful to watch the impostors do poses. He does admires them when they tell him of their mission to save a Distressed Damsel.
The second one is a seahorse girl who wants Dreambert to call her beautiful, despite her overuse of makeup. Dreambert gets completely irate every time he says it with dull emphasis.
Once Mario and Luigi venture deep into the Dream World version of Driftwood Shore expanded by Dream Eggs, Peach is revealed to actually be Kamek in disguise. Apparently, Kamek likes dressing up as Peach.
Kamek:"What? You think I just wanted to wear this? Actually... Yeah, you know, this frilly pink thing is pretty darn cute, I must say. I mean, those blue robes are so DRAB. Sometimes I open the closet and just gag. ...Wait. HEY!"
After Neo Bowser Castle rises up/falls down causes panic in the island, a quick talk with every citizen reveals that everyone you can talk to never left their spots for several reasons:
The Toads at the park ignore the Brock tours guide's warning to evacuate because they think it's an obvious marketing ploy of the island's attractions.
The Brickles at the park are quite confused as to what to do, but they're pretty indignant that their boss told them to just ignore the floating castle of doom in the sky.
The yellow Yoshi at the park laments that the trees didn't have any food on them after the earthquake took place.
A Toad exclaims that the fall of the castle was caused by him and congratulates himself for it, then adds that the brothers had some input in it.
Bedsmith's unsettling advances to nap on the bros. and especially Dreambert.
Speaking of him, the avid Pi'illo collector has several nerdgasms any time the bros. show him a new Pi'illo trinket.
In the ending, Dreambert was able to gather all of the fragments of the shattered Dream Stone, and asks the Zeekeeper to restore it. The Zeekeeper then turns the dust into an enormous floating coin. Dreambert's reaction is hilarious... and then the Zeekeeper breaks the coin into millions of regular coins. Dreambert staggers around afterwards in shock that the last treasure of the Pi'illo kingdom is gone, then begrudgingly admits that it's for the best.
At the Bonus Boss, once Bowser Jr. jumps out of the Clown Car, jump into it yourself. Laugh as you initiate a chase sequence where the Bros. are on the offensive, chasing Bowser Jr. down using his Clown Car and throwing junk at him.
After Grobot begins to hurt Brickle, his employees rush to the rescue and say this:
Employee #1: Boss Brickle!
Employee #2: Don't give up!
Employee #3: I need a raise!
And then after Brickle gets thrown:
Employee #4: You OK?
Employee #1: Boss Brickle!
Employee #2: LIVE, dangit!
Employee #3: Can I have next weekend off?
Luigi's reaction upon Bowser Jr. entering the Battle Ring.
When Bowser enters the Dream's Deep:
Bowser: *to Antasma* So what's the deal here? You Peach's kidnapper?! Gwahahaha! You're just a little baby bat! I could wear you as a brooch or something!
Mario attempts to save Peach; Bowser proceeds to punch Antasma.
Bowser: BAM! Seriously! That was IT?! What a total wimp!
Peach: Mario! We need to get out of here! Let's return to the real world!
Bowser: GWAHAHAHA! Good plan, toots. Time to fight, Mario! It's MY turn to kidnap her! It's Kidnapping Peach II... The Bowsering! TIME TO LOSE!
Antasma flies into Bowser's face; Antasma screeches.
Bowser: Wh-what's that?! WHAT IS ON ME?!
Prince Dreambert: No! You mustn't! Antasma!
Antasma screeches again.
Bowser: ARRRRRGH! Geddoff bee! Right dow!
Antasma: Vee go now! SCREEECH! Back to the real vorld!
Bowser: St-stop it! Get...OFF!
Antasma: SCREEEK! I vanted to steal Peach's power... But I changed my mind! You are much stronger... and evil! SCREEEONK! Vork with me! SCREEEP!
Bowser: Blech! Say it, don't spray it, dingbat. I don't "vork" with anyone! Get real!
Prince Dreambeart: End this... at once!
Antasma: SCREAAARK! Silence! *to Bowser* I can make your vishes come true. SKEEELK! Make you...SCREE...stronger than your vildest dreams!
Bowser: Huh?! What are you sayin', batface?!
Antasma: Vell, I will give you new moves. SCREE-EEK! Use them to crush your red and green enemies!
Bowser: Hmmmm... My old moves ARE feeling a little stale.
Antasma: All I ask in return is your cooperation. SCREEEK!
Bowser: If I say yes, will you quit screeching like that? You sound like a beached Blooper. *to Mario Bros.* GWAHAHA! I've got bad news, Super Loser Bros.! Big, bad Bowser's about to get even big-badder!
Prince Dreambert: Antasma, no!
Antasma: SCRAAAEERRK! Vee vill be unstoppable!
Bowser: LET'S DO THIS!
Antasma screeches one more time before boss battle ensues.
The Law of Pajamaja manages to be a funny song. This song, combined with the BEEFY Massif Bros and the absurd stories of the Muscle Lords, creates an unbelievably hilarious mood for Mt. Pajamaja.
Luigi's thoughts generally contain thoughts about how he wants to help Mario and be a hero... and the occasional "I fightghosts!"
After you defeat Torkscrew, the beast finally spits up Britta. Several workers come over and start lamenting as the screen fades to black and dramatic music begins to play. Then suddenly she says "I ain't dead!!" before getting back up and yelling at her workers.
One of Big Massif's disciples, Beef Cloud, fights the Mario Bros., by sleeping through the entire battle (while healing his health).
The Bros. encounter Mammoshka on Mount Pajamaja and try to avoid awakening him by tiptoeing. They do well at first... until Luigi sneezes and wakes up the beast.
The Elite Trio's conversation before their boss battle:
Private Goomp: Hoo boy! It's our big chance!
Corporal Paraplonk: For real, guys, if we can finish them here... I don't wanna jinx it, but PROMOTION CITY!
Private Goomp: Wait, what? I thought you said our career paths were already solid!
Corporal Paraplonk: Yeah, listen, about that... ... Timt out! Strategy meeting! Mario, we need a second!
Private Goomp: Stay RIGHT there!
Corporal Paraplonk: Look, we're already honor guards. Right? But if we nail this fight... We are talking about sitting at the big table! In head-honcho chairs!
Private Goomp: H-head honchos?! You mean we might even be Kamek's superiors?!
Corporal Paraplonk: YES, man! We could even be BOWSER'S superiors!
Private Goomp: Oh, wow! Let's go stomp those guys! I would LOVE to boss around Bowser! *all three race back to the Mario Bros.* Mario! We're back! Thanks for waiting! Hey... Is he DOODLING? Don't doodle at us! ... HONCHO TIME!
Pi'illodium counts as this:
Pi'illodium: Analysing foe potential... Chance of my victory: 120%
Pi'illodium: Boot: Self destruct.
Pi'illodium: Close call.
Pi'illodium: Uncertainly rising.
Pi'illodium: Cue beg mode.
Pi'illodium: Activate: regret.
Pi'illodium: Query: self-worth.
Pi'illodium: Return in: 1,000 years!
Pi'illodium: Foe still active: Why?
Pi'illodium: Laugh! Victory!
Walker Guys. They're tiny Shy Guys walking a huge Chain Chomp... except that in battle, it's less "walking" them than "hanging onto the chain for dear life as the Chomp throws him around".
Out of Canon
A funny case of irony. This game marks Bowser Jr.'s debut in the Mario & Luigi series, and it's a 3DS title. What other Mario spinoff series title did he make a debut on that had a 3DS release? Paper Mario: Sticker Star.
Even moreso when one considers that, like with Sticker Star, some folks at Nintendo tried to engage in Executive Meddling—though Alpha Dream moreso rejected the outside input than the former. They must just really like Jr. over there.