The change will probably happen around 2007-ish, when longhorn comes out. There's an upgrade test if you go the 2000 route, info here:
http://www.microsoft.com/learning/mcp/mcse/windows2003/ but your probably best, if your starting fresh, going right to 2003 server.
As far as certifications in general, one thing I can tell you is if you get a position somehwere, look at what they're using, and try and get certified in that. An MCSE may not do much good in a unix shop; but you can leverage your experience and accessability to the technology to improve your skills (and maybe even earn advancement).