At the Microsoft Learning booth yesterday at IT Forum (by the way, if you're in Barcelona and you're reading this, come by our booth in the Ask the Experts session... we somehow have a basket full of tiny cookies with MCP logos on them--really a 'don't miss'...) I got a lot of questions on what to do if you hold a Server 2000 or 2003 certification or you're part way through a cert path.
The rule of thumb is: get certified on what you're using now and will be using in the not-too-distant future. For example, if your organization is on 2003 and plans to stay there -- then completing your 2003 credential, or even starting out from scratch, is the right idea. On the other hand, if you haven't started your 2003 track and you KNOW you will be moving to Longhorn Server right away, then you might want to wait and start the new certification path when it becomes available.
About Longhorn Server certifications... there's not much to say yet. But if we were to say something, it would be:
A one-time MSL employee, David Lowe, was interviewed on LS, check it out: An insight into Windows Server "Longhorn". PS i believe i'm always supposed to say "Windows Server, codename 'Longhorn'" but I forget and say Longhorn instead. Don't tell anyone.