The Windows subkey stores configuration data for the programs running on the Win32 subsystem. The subkeys of the Windows subkey represent versions of the Win32 subsystem, such as CurrentVersion. Each version subkey contains subkeys representing programs that run on that version of the subsystem.
The Windows subkey in HKEY_CURRENT_USER stores entries that apply only to the current user of the computer. There is also a SOFTWARE\Microsoft\Windows subkey in HKEY_LOCAL_MACHINE that stores entries that apply to all users of the computer.