At this point it depends on what you are doing. Let's start with explaining the certs, as MS has changed their naming and certification schemes in the past couple of years.
In the old system there were basically only a handful of certs available. You had:
Microsoft Certified Professional (MCP) - you earned this by passing any MS certification exam in the NT4, 2000, or 2003 track.
Microsoft Certified System Admin (MCSA) - You earned this by passing 4 exams (two related to 2003 networking, one for a client OS, and one elective exam)
Microsoft Certified System Engineer (MCSE) - You earned this by passing 7 exams (four related to 2003 networking, one for a client OS, one a design exam, and one elective exam)
There were also specializations for Security or Messaging that you could earn with your MCSA/MCSE that required additional exams.
Now, under the new certification scheme (which started with Windows 2008, more or less) the MCP, MCSA, and MCSE and retired. You can still earn those certifications, but only by taking Windows 2003 exams. The new certs are:
Microsoft Certified Technical Specialist (MCTS) - You generally can earn this by passing a single MCTS exam related to Windows 2008, Vista, Windows 7, etc. There are also MCTS exams for Sharepoint, Exchange, Desktop Support, SQL, etc.
Microsoft Certified IT Professional (MCITP) - There are many variations of this certification depending on what products you are looking at. Depending on what technology you want to be certified with it can be 3-5 or even more exams to earn one of these certs. In the Windows 2008 space there are MCITP: Server Administrator (roughly analogous to MCSA and can be earned with three exams) and MCITP: Enterprise Administrator (roughly analogous to MCSE and can be earned with five exams).
So depending on what you want to do, there are a number of options. If you want to pursue the Windows 2003 certification track then you would look into MCSA or MCSE. The following is purely my opinion, but...
I personally would be reluctant to begin the MCSE or MCSA tracks right now. Windows 2003 is still widely deployed, but companies are moving towards 2008 and the 2003 certification track isn't really much of a help going forward. Besides, you can earn an MCITP: Server Admin cert by passing just three exams, compared to a minimum of four exams for an MCSA. If you wanted to earn a 2003 cert, I wouldn't recommend going any further than MCSA. I would only recommend that someone pursue an MCSE at this point IF their employer were requiring it OR if they had already completed a significant part of the certification track OR if they had the knowledge and experience to be able to knock the exams out in the span of a couple of weeks.
So if I were starting from scratch now, I'd probably go with the MCITP:Server Admin. You will have to pass two MCTS exams (networking and AD) plus one PRO exam (Server Admin) to earn the cert. But the two MCTS exams also count towards the MCITP: Enterprise Administrator. If you have the MCITP: Server Admin, you only need three more exams to upgrade to the Enterprise Admin cert.
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CompTIA A+, Network+, Server+, Security+
MCTS:Windows 7
MCTS:Hyper-V
MCTS:System Center Virtual Machine Manager
MCSE:Security 2003
MCITP:Enterprise Administrator