These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
"I was the one who added the nuts to that statue!"
This whole concept of this game is screaming with Accidental Innuendo. The Bros are "inside of Bowser's body." They have to "stimulate" his body parts. If you have a dirty mind, you'll be snickering all throughout this game.
Especially hilarious when, finding Bowser's funny bone near the beginning of the game, Starlow overtly says "If we can stimulate this thing, something'll happen...". Now take it out of context and try not to grin...
Big Lipped Alligator Moment: The giant Piranha Plants. They're not actually blocking your path, as after you beat them, you land back on the ground and go a different way to get to where you need to go next. Their only purpose is to introduce the Chest Station mechanic.
The Magic Window for the Brothers. Its damage would potentially be infinite if not for that pesky thing called "human reaction time," as the bros constantly speed up as the attack keeps going. Still, it can rack up more hits than any other move in the Bros' arsenal before its speed ramps up too much.
The Spin Pipe is less SP-expensive than the Magic Window, and fairly easy to do if you keep your eyes glued to the end of the pipe as it spins, and still positively devastating even in the final battles.
Magikoopa Mob or Koopa Corps. for Bowser. The latter especially since done perfectly, it will do damage comparable to even Broggy Bonker for less SP.
Broggy bonker, to an even greater extent.
Mighty Meteor in the Gauntlet. It gives you more powerful items when used than the game means you to have available. Really useful vs Dark Star or Bowser X.
As far as gear combinations are concerned, DX SP Socks and a Budget Charm on Mario gives you incredible special move usability, and the Delicious Gloves (Healing items are twice as effective) mean your opponent better kill you in one turn, or SUPER NUT! For Bowser, the Hunter Band is effectively a vampiric power-boosting item which can give up to a 30% attack bonus. It's pretty terrible against bosses, though.
The Intruder Fangs give Bowser two turns per round. Of course, you get them by getting Bowser to Level 40, and the game is usually finished at a much lower level, so by the time you receive them, you've probably already beat the game.
Bowser equipped with the King's Shell (his best armor which raises his defense greatly and his punching power by 30 percent) and his Intruder Fangs (which allow two actions every turn) combined with Broggy Bonker (his ultimate attack) being used both times makes the rest of the game into a joke.
Another Game Breaker is the Giant Shell accessory. Its description says the wearer takes no damage from hits that do less than 20% damage than the wearer's overall HP. Problem is, most attacks in the game don't do that much damage with enough defense investment. Equip this on one of the brothers and you can ignore them for the rest of the game except when attacking with them. In fact, if your defense is high enough, you won't have to bother with defense increasing equipment.
Most bro-targeting attacks can be dealt with simply by dodging/countering with both Bros (as opposed to pressing the button of the brother being targeted). There are moves that explicitly punish this tactic, but only occasionally.
Fawful's line "Beef? I am lacking in beef. Fawful is beefless" becomes much funnier after Dream Team introduced the Massif Bros., who barely talk about anything else except beef.
Some fans were joking that the third Mario & Luigi game would be a "platformer"-like game, similar to Super Paper Mario, the third Paper Mario game. Well this game still has the 3rd Person mode, but inside Bowser, you get to experience it in a 2D aspect, similar to Super Paper Mario. This was passed onto Dream Team as well.
Ho Yay: Bowser locking his mouth on Midbus's snout and inhaling his breath for an extended period of time. True, Midbus was a frozen block of ice and Bowser was burning up inside after swallowing the Dark Star, but it was still hilarious. Though Bowser does say something to the effect of "That was gross" after doing it.
Idiot Plot: The plot revolves around Bowser putting suspicious things in his mouth, twice.
Magnificent Bastard: In a way you've got to hand it to Fawful when you think about it his plan only fell through because he underestimated Bowser's ability to sneeze.
Memetic Badass: This describes Bowser in general, but this game takes it to new levels.
Some of the Fawfulized enemies fall into this. Not only do they all sport his glasses and possibly-now-creepy smile, but there are also the implications that arise for Chain Chawfuls that you can liberate by getting rid of Fawful's influence instead of just beating them up like usual.
Bob-Omb Blitz deserves a very special mention. You need to line up all of the Bob-Ombs to Broque Madame's hitbox in a 2-3 second time limit, with the amount of Bob-Ombs on screen increasing and the time limit decreasing. Three non-perfect attacks, you're done. There's a reason her bed looks like a grid. Without the lines on the bed, it's near impossible.
That being said, the rewards are proportional: clearing all of Broque Madame's challenges with an A nets you the King's Shell, Bowser's best armor, while finishing the Cholesteroad's Jump Helmet with an A will give the Daredevil Boots, and finishing all of the challenges, again, with an A ranking, gets you the Master Wear, the bros' best armor.
The Scrappy: Starlow gets quite a lot of hate for being an annoying Exposition Fairy. Definitely intentional, since Bowser gets increasingly annoyed with her as well as the game goes on.
Not many people like the way you have to blow into the DS's mic in order to breath fire during the Giant Bowser parts. This is especially frustrating in That One Boss mentioned below.
That carrot minigame with the Wiggler in Dimble Wood.
The pollen minigame can also fall into this; the controls are finnicky, aiming the pollen into the correct section of the wall can be difficult, the blue pollen makes you drop coins and you can only get hit 3 times before you have to start all over again.
When Bowser's back is healing, you are told to wait for a while and come back later. Most people would close the DS and go do something else, but the DS goes into sleep mode when you close it, and sleep mode does not count time. If you leave the DS open for about 10 minutes, the task will complete, but if you carry it with you and briefly check on it every day, it could take months.
If your DS microphone is wonky, pretty much any of the giant Bowser fights are this. The microphone test might tell you that everything is working, but the action commands are another story. Even an air compressor blowing into the mic at various flow rates and time intervals can't help you if your DS mic is crap. This is especially important in:
Giant Bowser's fight against the Fawful Express. Not only are the attacks powerful and hard to dodge, but you have a limited amount of time to win the battle, or it's an instant death. Also you can only use your flame because the train is too low to punch, and you have to destroy several obstacles along the way. If you beat this on your first try, give yourself a pat on the back. If it took you a couple of tries to beat it, don't feel bad and just be happy it's over at last when you finally achieve your victory.
The Mario & Luigi fight between Memory M & Memory L. What makes these two bosses hard as that they seem to copy the Mario Bros.' statistics: Mario is more powerful, and Luigi has more HP. Mario's two attacks are quite frequent: one of them has him get a Super Star and become invincible, ramming through the Bros. (on some occasions, a coin will pop up and Memory M will follow it). His other attack is growing huge and breaking bricks so that the Mario Bros. have to break the remaining parts fully. Memory L's attacks appear less often but are scarier than Memory M's: One of them is throwing a hammer in the sky so that one of the Mario Bros. have to whack it back; the other one likely requires the most timing, as Memory L will get pursued by a Memory Boo: he'll jump over the players, but the Memory Boo won't. You want to know what's worse? If you defeat Memory M first, Memory L will simply revive him (thankfully only a little bit of HP, though). Because of this, you may think to defeat Memory L first so that he can't revive Memory M when defeated - but Memory L is just a coward as Luigi, and will often run off the battle screen, and will likely not return until Memory M if defeated. Get ready for the pain.
Junker. His first couple attacks aren't too hard to dodge - but then he sucks up Luigi and puts him in one of the Junker Cans. Now you have to use Mario to defeat the Junker Can containing Luigi, but Junker and his minions will use a wide variety of attacks to keep you from freeing Luigi - worse, if Mario is defeated while Luigi is still in one of the Junker Cans, the battle will instantly end. It doesn't help that his other attacks do pretty high damage as well...
They Wasted a Perfectly Good Plot: All of Giant Bowser's boss battles were with machines of some sort, but never against a giant Midbus. They could have worked in Fawful using the Dark Star to power him up to monstrous heights and gives us a bit of Godzilla homage.
Viewer Gender Confusion: It's mentioned twice, early in the gamenote :"NOT how to treat a lady!", and during the Flab Zone quiz, that Starlow/Chippy is a girl. Few people seem to remember this.