Custom IOS, aka cIOS, are third-party IOS files that are installed on the wii. Most cIOS's are used for pirating. They are often made by using a base IOS with desirable features, such as USB support or Rockband microphone support and modified to install to a different slot such as 254 and then add extra features, such as restoring the trucha bug and adding piracy related functions.
With the discovery of the HW_AHBPROT register, new official IOS revisions with USB2 support, and integration of the HW_AHBPROT into the Homebrew Channel's access permissions field, most homebrew should no longer depend on a modified IOS in order to do things which normally would require them. Thus, homebrew which requires custom IOS should be removed and replaced with less invasive, more modern alternatives.
Other software technically installs custom IOSes, but these IOSes do not have the piracy functions commonly associated with cIOS.
- Better hardware control with Wii-Linux
- Lower risk NAND/SEEPROM flashing
- Custom WiiConnect24 implementations such as RiiConnect24 or WiiLink
Due to its heavy links with piracy, the word cIOS is generally avoided by most of the homebrew community, instead preferring more generic terms such as "patched IOS" when writing programs that require them.