The "HKLM\SOFTWARE" subkey contains software and Windows settings (in the default hardware profile). It is mostly modified by application and system installers. It is organized by software vendor (with a subkey for each), but also contains a "Windows" subkey for some settings of the Windows user interface, a "Classes" subkey containing all registered associations from file extensions, MIME types, Object Classes IDs and interfaces IDs (for OLE, COM/DCOM and ActiveX), to the installed applications or DLLs that may be handling these types on the local machine (however these associations are configurable for each user, see below), and a "Policies" subkey (also organized by vendor) for enforcing general usage policies on applications and system services (including the central certificates store used for authenticating, authorizing or disallowing remote systems or services running outside the local network domain).
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Individual settings for users on a system are stored in a hive (disk file) per user. During user login, the system loads the user hive under the HKEY_USERS key and sets the HKCU (HKEY_CURRENT_USER) symbolic reference to point to the current user. This allows applications to store/retrieve settings for the current user implicitly under the HKCU key.