WinterBoard acts as a file replacement extension for iPhone OS based on Mobile Substrate, both of which are developed by saurik. It is often used for theming GUI elements, such as app icons. Check saurik's website for more information.
It works by injecting replacement files dynamically but without actually replacing the files, though it appears to the iPhone that the files have been replaced. Should Mobile Substrate crash, the files will no longer appear to be the changed ones and the theme will be removed, except for a few images that iOS caches, such as the Notification Center and app switcher backgrounds.