Use the "guest customization" feature when cloning or deploying from template, and "Generate a New SID." It works well. In addition to any possible application-specific SID bindings, I've seen Windows Update failures in WSUS environments. Mark Russinovich makes note of that as well:
"Note that Sysprep resets other machine-specific state that, if duplicated, can cause problems for certain applications like Windows Server Update Services (WSUS), so MIcrosoft's support policy will still require cloned systems to be made unique with Sysprep."
Blogs - Mark's Blog - Site Home - TechNet Blogs
If you for some reason decide not to use VMWare's Sysprep invocation via guest customization, you can do it manually:
Sysprep (Generalize) a Windows installation