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Custom firmware, also known as CFW, is an unofficial firmware developed for devices. Despite the name, it is most often a program that patches an official firmware to add new features, rather than being an entirely new one.
Nintendo 3DS
The most commonly used CFW is Luma3DS. It is the only one still in active development in 2022.
Others that were commonly used in the past were ReiNand, corbenik, CakesFW, and rxTools.
Wii U
The Wii U has a CFW called Aroma.
Other CFW's for the Wii U that were used are Haxchi (and to extension, Coldboot Haxchi), Mocha, and Tiramisu.
Nintendo Switch
The most popular custom firmware currently is Atmosphère. Previous firmwares include Reisyukaku's ReiNX and a fork of Atmosphère called SX OS.
Atmosphère is currently the only actively maintained Switch CFW.