The World of Nothing in Super Paper Mario is creepy enough as it is, with the entire world destroyed (Or, more accurately, erased), but then you go to the Underwhere, which is the land of the dead. None of the people from Sammer's kingdom there. Then, a little while later, you find out that the land of the dead is going to be erased too. ... This is for kids, right?
There's a Whacka in this game, which just so happens to be the last of his kind. You can whack his head to gain bumps, which make for amazing healing items (and an important recipe ingredient). Whack him too many times, you kill him. However, the Flipside Arcade has a lot more Whacka bumps for you to buy. Wait, I thought that one Whacka was the last of his kind. Where did they get the bumps... Ohfuck.
At the beginning of the game, Count Bleck sucks Bowser's army into his castle with a black hole. When you reach Castle Bleck, there aren't a huge number of them, but there are a lot of Dry Bones...
After you complete the game, you can revisit all of the worlds you've visited...including Castle Bleck. Which is in the heart of the Void. Which means that the Void, and therefore the prophecy of the Dark Prognosticus, still exists.
If it makes you feel better, the opening title sequence clearly states that Super Paper Mario is the tale of the Dark Prognosticus's "last owner". So unless the book suddenly gains the ability to act on its own accord, it can't hurt anyone ever again.
Dimentio wants to destroy all of existence. That means every universe that exists. ...We are one of them. Be glad it's just a work of fiction.
Ordinarily, in games like this you save the world before it is destroyed. But in SPM you don't. You get to see all the previous worlds and people you visited whipped out of existance. This game made Luigi an accessory to omnicide.
The afterlife is a seperate universe, which the dimension-bending antagonists can enter and leave at will. That's right: No matter how many times Dimentio is killed, he can instantly resurrect himself.
Presumably, he's just biding his time until another chance for multiversal destruction pops up.
Or probably there is a difference between going in and out the Underworld while technically alive, and going in and out while technically dead.
Maybe even creepier is the fact that Dimentio is shown to be able to simply teleport people to the Underwhere. Even if you're completely, 100% invulnerable, he can still insta-"kill" you.
The Pixls are hilarious Cloudcuckoolanders, until you realise that they have been locked up in chests for thousands of years and the isolation has probably driven them insane.
Mr. L.'s basic personality traits are sarcasm, greed, jealousy, and cockiness. These traits have appeared before as Luigi's faults... All Mr. L is is the personification of Luigi's personal flaws, the traits that keep Luigi from being too powerful. As a result, he can never win, because he's just an exaggeration of someone's most negative qualities.
The Mushroom Shakes only appear in this game and no other games. Shigeru Miyamato originally wanted Donkey Kong to be a Popeye Game. Popeye normally powers himself up with cans of spinach. Maybe it's actually a subtle Popeye reference!
The world entrance doors on Flipside Tower are in Roy G. Biv rainbow order:
Lineland's door is red, Gloam Valley's door is orange, the Bitlands' door is yellow, Outer Space's door is green, the Land of the Cragnons has a blue door, Sammers' Kingom's door is indigo, and the Underwhere/Overthere's door is violet/purple.
The Primordial Fruit can be used to make a Town Special dish, and a Whacka Bump can be used to make a Roast Whacka Bump. However, both of these dishes actually heal less HP than their ingredients. This is representative of the Cragnon's wasteful nature, as both those dishes are said to be Cragnon-based.
This is the first game to feature direct combat (ie. jumping on people) rather than turn-based. Why? Because it's the first to take place in a different dimension, that's why.
The title screen. It shows all four of the heroes, but guess which hero you DON'T have in your party for the final boss.
In the very first chapter, you cross two bridges on the way to the final check point. The first is a simple wooden bridge, but the second is much more grandiose and overall better looking. So what's with the big discrepancy in quality? Well, try flipping dimensions around them. The simple bridge is fully functional whether you're in 2D or in 3D, but the pretty bridge is totally flat and can only work for people in 2D.
The fact that each of the two people who run these bridges is an Expy of Mario and Luigi (respectively) makes sense if you consider their characterization in previous Paper Mario games. The expy of Mario, the always reliable Heroic Mime, runs the simple bridge, and the expy of Luigi, who is a less successful hero yet a bigger braggart, runs the flashier yet less efficient bridge.