.NET 3.5 and 4.0 on Windows 2008 R2

Try running aspnet_regiis /i from the 21006 framework folder. That should re-register it with IIS7.

It should be possible to script such a process, I would probably start with PSH as it has inbuilt XML support and access to .NET (useful for generating new keys if they are being specified).

But the first thing is to get the list of virtual directories at which to start. This is mostly easily done with appcmd:

# Use array constructor to force an array, event with only one result
# format: VDIR "name" (physicalPath:path)
$vdirs = @(C:\Windows\system32\inetsrv\appcmd.exe list vdir)
$vdirs = $vdirs | Where-Object { -not [string]::IsNullOrEmpty($_) } | Foreach-Object -Process {
  if ($_ -match "physicalPath:([^)]+)\)$") {
   $matches[1]
  }
}

At this point $vdirs is an array of folders mapped to IIS.

Within each of these search for web.config files:

$configFiles = $vdirs | Foreach-Object -Process {
  Get-ChildItem -Path $_ -Recurse -Filter "web.config" | Foreach-Object -Process { $_.FullName }
}

Which is an array of the full path names of the web.config files. At this point you can use PowerShell's XML support to examine or update any part of the file you like