What do you mean by "Server Class"? Are you asking how to create a custom Server Control or just a general class library?
The runat attribute is used for individual controls and not for entire applications, example:
<input type="text" id="foo"> <--this is a standard HTML input box
<input type="text" id="foo" runat="server"> <--this is a standard HTML input box that i can now access in code
hth.
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