A villainous one from the beginning of the game: Bowser storms Star Haven, kidnaps the star spirits, and takes the star rod, all without any sort of opposition. He then proceeds to use this power to come far closer to actually KILLING Mario than any other instance in the entire series. If it's not entirely clear how much of an accomplishment that is, not even the end of the universe managed to kill the plumber.
Sometimes you can get rare Lil' Oinks. The Golden ones drop Ultra Shrooms and Silver ones drop Jammin' Jellies. You can combine the items to make the best healing item in the game, the Jelly Ultra.
Seeing Dry Dry Ruins come out of the ground for the first time.
Defeating The Master at full power in the first game. The Crowning Music of Awesome that accompanies it makes it even better.
Defeating Tubba Blubba and freeing the Boos.
If you don't use Watt in the room right before General Guy, Shy Guys will swarm you and slap Mario around.
Everything about General Guy; he made an awesome, fun boss with great music.
Kolorado tries to attack Lava Piranha while it's on fire.
Misstar saving the party from the erupting volcano.
Helping the Sun rise in Flower Fields.
Peach gets several throughout the game for refusing to stay locked up and trying to help Mario however she can by spying. She can even send him powerful items and badges, and the Sneaky Parasol event makes it better.
The citizens of the Mushroom Kingdom all wishing for the Princess to be alright as you ascend to the final level. Even the one who just wants to eat Shroom Cake.
During the last chapter's first cutscene, the game hands us one. After Kammy Koopa tells Bowser that Mario has saved all of the Star Spirits, he ties up Princess Peach and decides to kill Mario himself. Twink of all people jumps in to try and save Peach by attacking the Koopatrol. Sure, it didn't work, but hey, it was awesome nonetheless.
Peach wishing for the Star Beam to gain power after Bowser cancels it out.
Another villainous one by Kammy: she displays Genre Savvy all throughout the game, which includes not trusting Peach's answers when Bowser questions her about Mario's weaknesses and seeing through Peach's clever disguise late in the game. On top of all that, she subverts a major villain cliche by preparing a secret weapon for Mario's arrival, even saying, "Do you really think we were foolish enough to just sit back and watch as you save the Star Spirits?"
Paper Mario: The Thousand Year Door
The Glitzville chapter. Battle tournaments, screaming fans, and a super-creepy mystery? Badass.
Not to mention getting to name a Badass Adorable Yoshi and if you know the waiting how many minutes trick to wait before running from a Hopeless Boss Fight you can also get the color you want the Yoshi to be as well.
During the final battle, everyone around the world starts to cheer for Mario. They're on the edge of despair and plunged in darkness, but seeing the Crystal Star show up in their area reminds them of Mario's impact on them in his adventure, and it revitalises their hope. It definitely reflects on the player too— you've come so far, and seeing all these characters rooting for you and showing the progress you've made, is just amazing. It definitely counts as a Tear Jerker and a Crowning Moment Of Heart Warming all at once.
The climax of Chapter 6, in which the little dust bunny things from the day before invade the train and take almost every passenger onto the roof, at which point they merge together. It's Mario vs. a multitentacled monster on the top of a train known for extremely high speeds. Combined with the music, it's absolutely amazing.
Anytime Mario and company Super Guard successfully, the awesomeness of the SG being directly proportional to the flash and power of the attack. In some cases, there are opportunities for Awesome Moments against weak enemies, such as if Mario Super Guards against the Goomba Bros.' sneak attack during the opening bout of the Glitz Pit. (Depending on the requirements, Mario may be free to whale on them in his next opening turn, which only amplifies his entrance to the put).
In Chapter 8-2 of Super Paper Mario, you have to fight Mimi (AGAIN) at the end, but this time you can only play as Peach. Nothing is better than kicking the most annoying boss's ass using Peach, of all characters. And to top that off, creepy but awesome music plays in the background.
Tippi: Not everything is set in stone. Some things we decide for ourselves.
Bowser's line makes it even better:
You believed in your prophecy, and we believed in mopping the FLOOR with you!
Oh yeah, and Dimentio's Taking You with Me move that could only be canceled out BY MARRIAGE. I just find it cool he didn't rely on the heroes being dumb enough to do absolutely nothing, as most tend to do.
Paper Mario: Sticker Star
Bowser defeats Mario so thoroughly at the start that he's folded and crumpled up when Kersti finds him.
One Toad at the beginning of the game is hiding behind a bush waiting to ambush Bowser.
Bowser Jr. uses paperization to wad up a bridge Mario needs to cross, then throws it to the top of a cliff that can only be reached from the other side of the bridge. A bunch of Toads save the day by stacking together to form a staircase.
Any time Mario warps reality with the power of Stickers, Paperization, and Things.
At the end of World 1, a team of Goombas show resourcefulness with their papery bodies and group together as the boss. Suddenly they're a Not-So-Harmless Villain.
Goombas and Koopas have skills to back up their words this time around, and gleefully mock Mario as they show off their sticker power.
Restoring the oasis with the Faucet in World 2.
The unveiling of Drybake Tower in World 2.
Wiggler swimming across a poisoned ocean to get Mario and Kersti to the island.
The boss of World 3, Gooper Blooper, getting Hoist by His Own Petard, should the player use the proper Thing sticker (sponge). Mario gets an awesomeTheme Music Power-Up and the boss won't be able to hit him. Kind of cathartic after all the problems the boss has caused for the forest.
The final boss battle. Bowser just keeps throwing wave after wave at you, culminating in the prerequisite One-Winged Angel. All of this even more awesome by getting a Theme Music Power-Up at the end, thanks to Kersti's sacrifice, and going to town on the boss.