Visual Studio 2005 and 2008 are both smart enough to look in the version of the Windows SDK included with those compilers, but I'd never found a way to change the default version. Until now.
The Windows SDK comes with a utility called the Windows SDK Configuration Tool. You can find it in your Start menu.
When you run this, you can set the default SDK to be whichever version you want. Then Visual Studio will automatically reference that version of the SDK without any need to manually update project directories.
[Update 8/31/2011]
Visual Studio 2010 does not seem to pay attention to the Configuration Tool. Instead, this appears to be set on a project-by-project basis in Configuration Properties/Platform Toolset. After doing so, you may be able to fix some schizophrenic behavior by updating the MSBuild information too. Take a look at the following registry entries. (Thanks to the tip from http://geekswithblogs.net/rob/archive/2010/09/17/integrate-the-windows-sdk-v7.1-with-vs2010.aspx)
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\MSBuild\ToolsVersions\4.0
- FrameworkSDKRoot (REG_SZ)
- $(Registry:HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Microsoft SDKs\Windows\v7.0A@InstallationFolder)
- SDK35ToolsPath (REG_SZ)
- $(Registry:HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Microsoft SDKs\Windows\v7.0A\WinSDK-NetFx35Tools-x86@InstallationFolder)
- SDK40ToolsPath (REG_SZ)
- $(Registry:HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Microsoft SDKs\Windows\v7.0A\WinSDK-NetFx40Tools-x86@InstallationFolder)
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