The statement and subsequent questions deal with 3 completely different areas of Microsoft technology - Vista, Servers running IIS and Web App Development - and there are different certification offerings for each. Vista certifications naturally are geared towards the desktop, since Vista is after all a Client OS. Look back at your XP certs, and you'll find the same offerings. One exam for the OS itself, and 2 exams for desktop support. Vista exams follow this same pattern.
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For current implementations of IIS on Windows Server 2003, your trusty MCSE exams will do the trick. For any new server-related exams, we'll have to wait until Longhorn Server hits the scene. If the schedule holds true, we should see the new server OS later this year with exams readily available in early 2008. At that time, the MCSE will no longer be the flagship cert. It will not be retired by Microsoft, but it is due to be replaced by MCITP. Inside sources confirm that many industries outside of IT backlashed against Microsoft for calling their certified professionals "engineers." Can't say I completely blame them since chemical, civil and mechanical engineers require bachelor degrees.
As for web apps, you'll have to look towards Microsoft's new certification offerings. The Microsoft Certified Technology Specialist (MCTS) credential for Web Applications using the .NET Framework 2.0 requires 2 exams, 70-536, Application Development Foundation, and 70-528, Web-Based Client Development. Vista and server certs usually go hand in hand, but developer certs are held those with very different skill sets. Now if you are one of the few that actually has expertise in both OSs and programming, then you are in a very select group indeed. For more information, visit the Microsoft Learning Site.
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