See tip 4016 for a Windows 2000 article.
Microsoft Knowledge Base Article 315688 contains the following summary:
The NTFS file system supports many volume- and file-level features that may cause
free disk space to be either misreported or reported as lost. You may notice this behavior if
an NTFS volume suddenly becomes very full, and you cannot find the cause or locate the
folders and files that cause the NTFS volume to become full. This behavior may occur if a user gains
malicious or unauthorized access to an NTFS volume on which either very large files or a high quantity
of small files are secretly copied, and then removes or restricts NTFS permissions on these files.
This behavior may also occur after a system malfunction or a power outage that causes volume corruption to occur.
This article describes how to check NTFS disk space allocation to either discover offending files and folders or locate volume corruption. This article is intended for users of Windows XP operating systems that support advanced storage features and troubleshooting methods.