Paper Mario: The Thousand-Year Door

Paper Mario: The Thousand-Year Door, released in Japan as Paper Mario RPG, is a console role-playing game developed by Intelligent Systems and published by Nintendo for the Nintendo GameCube. The Thousand-Year Door is the fourth game in the Mario RPG series and the second in the Paper Mario series.

Problems
Good - Minor Graphical Issues

Chapter 2 - The Disappearing Punio/Invisible Punie Problem (MINOR SPOILER ALERT): In the second chapter during the Great Boggly Tree dungeon, you come across two adjacent cells (one contains the Punie elder, the other contains 90 Punies). After you receive the red key to open the elder's cell and attempt to open it, you will most likely come across a very frustrating problem: Punio will disappear and leave you stuck in a zoomed-in screen, hindering any further progress in the game. Many frustrated Dolphin users have been searching for a fix to this graphical issue, but seemingly to no avail. There is a specific revision of Dolphin that WILL allow you to progress through this frustrating glitch however: DolphinIL SVN R4707. In this revision of Dolphin, players should find that Punio remains visible during the "cell-opening cutscene" and allows the game to continue normally. Unfortunately though, this revision does not fix another VERY frustrating problem: All but the main NPC punies (Punio, Elder, Puniper & Petunia) will be invisible the entire time, making it very difficult to manage all 101 of them throughout the long dungeon. The framerate will also suffer a significant drop in this dungeon, probably due to the amount of Punies (well, Punie shadows) following you around.

Chapter 5 - The Glitchy Toad/Pianta Problem (MINOR SPOILER ALERT): Near the end of the fifth chapter (right after the boss fight against Cortez) you find yourself forced to blow your way out of the Pirate's Grotto in the previous area before the boss which is filled with toads and the Pianta lovers. In most cases players will find that most of the toads (like the Punies in chapter 2) are invisible. When you blow through the crack in the wall with Bobbery a cutscene plays, showing the toad next to the hole attempting to leave the cave and suggesting everyone else do the same. Now here this problem seems to vary depending on the specific build of Dolphin you're using, but in any case during the "escape sequence", one of the visible characters will suddenly start glitching back and forth and will halt you from progressing any further (you do not regain control of Mario until all the others have escaped). Once again, DolphinIL SVN R4707 is the remedy, however in this case even using this revision the bug will still occur. Now to get through this troublesome glitch using R4707, all you have to do is continuously tap A until all of the characters have proceeded through the hole.

Gameplay Videos
Paper Mario The Thousand Year Door on PC - Dolphin emulator