A memorable moment in Super Paper Mario is the "many Dimentios" room in Chapter 8-3. Oddly, the Dimentios do not despawn when they are defeated. Instead, they fall into the void below the stage, where they remain frozen in pain forever.
Mario & Luigi: Superstar Saga contains a "Spanish Peach Protection" exploit. Normally, Peach gets kidnapped in a cutscene when Mario is distracted by Toadsworth. Setting the language to Spanish helps mash through Toadsworth's text so fast that Peach never actually gets kidnapped.
In Paper Mario, a bizarre and inexplicable detail is that some Dry Bones will be intimidated into not throwing bones at Mario if he is accompanied by Sushie specifically. No other partners have that power.
In the "Waltz of the Boos" theme from Super Mario Galaxy, the pizzicato arpeggio in the beginning and throughout the song spells out "DEADEAD DEADEAD". Whether the usage of the sequence "DEAD" for a ghostly theme is deliberate or merely a fitting coincidence is unknown.
In Paper Mario, Parakarry is a clumsy postman who joins Mario to find letters he lost. However, at the end of the game, Parakarry leaves, while the letters never actually get removed from Mario's inventory. This creates the humorous effect of Parakarry forgetting them once again.