You know, I just wrote a whole tip on this very subject called Certify now on Windows 2000 or wait for Windows 2003?. The short answer to your question is: if you want to get certified before the end of 2003, go Windows 2000; if you can wait until mid-2004, you can go either way. Let the platform in use on your job or at the companies where you'd like to work guide your choice. Windows 2000 stuff won't be "obsolete" for at least another 30 months, if history is any guide. Also, MS has defined some decent upgrade options this time around, and you'd only need to take two conventional exams to upgrade your MCSE from Windows 2000 to Windows Server 2003. If I were in your shoes, I'd go Windows 2000 now, and take the upgrade exams later in 2004.
Good luck, whatever you decide.
This was first published in March 2003