Hmm... I'm pursuing MCSE 2003 and have wondered if maybe I should have gone the 2000 route... I've been told by some guys with 2000 certs to just go for 2003 since it will obviously hold up longer. Of course if you go with 2000 you can upgrade it with just one more exam and have both. You can't do that with 2003.
Even still, I am going with the newer cert.