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.

Professor Frankly's Gate
The gate outside Professor Frankly's house turns into a cyan block, and then disappears when he is opening it to show you the Thousand-Year Door

Dance with the Invisible Princess
When TEC asks you to dance with the hologram of the Princess (end of Chapter 2), the hologram appears only if the EFB Copy is set to Texture.

Fuzzy Punies
In the Great Boggly Tree, all the Punies except for Punio, the Punie Elder, Punio's sister, and the fat puni will have strange effects and clones caused by rendering issues, which makes the Punies have a fuzzy look.

Sound Issues
Sometimes the background music isn't played or the L and/or R channels get desynced or muted. In extreme cases all sound in the game mutes, requiring you to restart the emulator to get the sound working again. DSP LLE should resolve these sound issues.