EXPERT RESPONSE
Given that Windows Server 2008 is due out next January or February, you're coming on the likely retirement of Windows 2000 credentials in the near future anyway. I'd recommend switching over to Windows 2003 at a minimum, or perhaps even waiting until after Windows Server 2008 ships and re-tooling on that new server operating system (and Windows Vista for the desktop). Given the amount of work involved in earning an Microsoft certification, you'll get a better return on that investment if you work on the latest and greatest platforms and credentials.
That said, if you don't expect to be working with the new desktop and server operating systems for at least another two years, it may still make sense to go after Windows Server 2003 based stuff, and then to upgrade your credentials for Windows Server 2008 and Vista once you get through the Windows 2003 series.
But if it were me, I'd go after the newest stuff right away.
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