In case you’re google-ing after this, it’s normal that the Windows Update for Windows Server 2003 x64 kb928416 takes a _very_ long time to install.
This update installs the 3.0 version of the .NET framework. During the install, you’ll see hardly no CPU usage, nor any I/O requests. But don’t worry, it’s working in the background. Took nearly 20 minutes for that single update to install on a x64 w2003 server here – and it got me just a little worried … but it installed fine, and is working properly at the moment.