This chapter can't possibly list all of the possible integration points in Windows that an application can take advantage of. Each integration point has its own requirement, which may vary from run-time calls into APIs, or one-time calls into configuration APIs.
Windows' design guidelines include guidelines for installation and removal of applications. The requirements of each application are different, depending on how it integrates into Windows, but the general guideline for removal is to remove any artifacts required by the application to run or integrate into Windows, and leave user-created files on the computer (or prompt the user to remove user-created files).
Much beyond hooking into Add/Remove Programs or Programs and Features, it is up to the application to decide how to configure and remove. This could entirely be written by the application developer (calling into the APIs to create registry entries, copy files to Windows system directories, and so on).
...