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.
Fridge Logic: A hilarious (and very fortunate) in-universe example. Right when Mario leaves Lavalava Island, Jr. Troopa shows up, having swam all the way there. He misses Mario and has to swim all the way BACK to Toad Town. When Mario fights Jr. Troopa at Toad Town Harbor, his HP will be halved at the start of the battle. After Mario beats him, Jr. Troopa will realize he could've just flown to Lavalava Island and back since he has wings.
The Dotwood Tree in Super Paper Mario. If you get hit by a Crayzee Dayzee mid-jump (and this is a very jumpcentric level), which you probably will, you'll probably end up falling a good distance and having to do large chunks of the level over again.
Chapter 2 in every Paper Mario game can get annoying pretty quickly. In the firsttwo games, it's because of the enemies getting noticeably stronger than they were in the first chapter without Mario having much of an advantage to match; in the third, it's because of Merlee's Mansion being tedious to get through (especially 2-3), not to mention having one of the biggest doses of Nightmare Fuel in all of Paper Mario; in the fourth, it's because the levels tend to be The Maze, at least one of them has some borderline-Guide Dang It moments, and the boss pretty much imprints upon you the game's (stupid freaking) boss weakness system.
Woobie: Shadow Siren Vivian is often wrongfully and mercilessly disciplined by her sister Beldam. If you feel like treating her right, well, Chapter 4 seems like the right time to start because Doopliss steals Mario's body and Vivian's sisters leave her alone while they slack off. She will join you after you console her, but eventually, she'll find out who consoled her, but she'll stay.