Plugins are special tools which can be run in-game. The game has to be dumped with either Vitamin or MaiDumpTool. All plugins have to be placed in the ux0:plugins folder.
Amphetamin by TheFloW

The very first in-game plugin - This simple plugins allows you to overlock the ARM clock to 444mHz.
Usage: Hold SELECT in-game.

rinCheat by Rinnegatamante

Multipurpose game plugin. Features include real-time cheats, cheats database support, decrypted savedata export/import and high-quality screenshots.
Usage: Press SELECT+START in-game.