Hi,
It all depends on what you are more familiar with. If you have been using Server 2003 for a while I would recommend getting your MCSE has you are familiar with it. Even though there are new certifications out there ie the MCITP Enterprise Administrator: Many companies will still be using Server 2003 and your certification will still be valid.
Now if you have never used Server 2003, I would recommend the next generation certs MCTS. If you want to start out with the Server side (2008) there is the Microsoft Certified IT Professional (MCITP) Enterprise Administrator and Server Administrator. These are comparable to the MCSA and MCSE of 2003 but not exactly the same.
Now if you have not used either Server 2003 or 2008 but are more familiar with XP or Vista I would recommend going with the MCDST: Microsoft Certified Desktop Support Technician, This is on XP
Or
MCITP: Consumer Support Technician and MCITP: Enterprise Support Technician. These will with the Vista Client...There will also be the same certs but for the Windows 7 clients.
Here is a link for the MCDST:
http://www.microsoft.com/learning/en/us/certification/mcdst.aspx Here is a link for the available MCITPs
http://www.microsoft.com/learning/en/us/certification/mcitp.aspx#tab2 Hope this helps.
Eric