No Managed Code
The code behind the .NET Framework is not modular enough to be broken up into just the components that Server Core will be able to run. (This might be added in future releases and looks to be reasonably high on the priority list.)
Not only does this mean you can't run any custom web applications you might have created, but you also lose access to some of the better management software that comes along with this generation of Windows, including Windows PowerShell (which used to go by the code name Monad). Server Core just isn't a .NET machine at this point, so for web applications and other custom software, you will need to deploy the regular, fully fleshed-out Longhorn Server edition of the operating system.
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