<p>I have a lot of classes in the App_Code directory could this be a problem? Would it build faster if it was in a separate library?</p>

<p>Any other tips?</p>

There's a decent article
here
. Items listed there are:
Do not disable batch compilation
Leverage Server-side Compilation
Move App_Code files into a separate class library project
Check for conflicting dependencies
Turn off AutoToolboxPopulate in the Windows Forms Designer options.
Disable validation for HTML editing