Had this issue appear when we Ghosted from a 36GB Server to a 147GB Server. Was running Sharepoint Services for internal use on the server, and none of the applications (administrative or otherwise) would run. Checked permissions, did all the Windows Updates. Notta.

Then I happened across a small Microsoft Issue when dealing with .NET1 and .NET2 on the same server.

Quick repair for .NET2:
1.) Start >> Run >> CMD
2.) cd C:\WINDOWS\Microsoft.NET\Framework\v2.0.50727
3.) aspnet_regiis -ir
4.) Reload your failing page

Quick repair for .NET1:
1.) Start >> Run >> CMD
2.) cd C:\WINDOWS\Microsoft.NET\Framework\v1.1.4322
3.) aspnet_regiis -ir
4.) Reload your failing page

As you can see the command is the same between the two versions of .NET. This fixed the issue, but it may not work in all cases. Check the permissions and the log files from IIS to see where the problem is.

[UPDATE]
The reason that the links between the applications and .NET failed was when I did an overlay Windows repair after ghosting to a new machine. Look up Ghosting Issues for more details.