Thanks to Chris Pietschmann 

 
There is a way to partition the App_Code folder into sub-folders, one for each set of code files written in the same programming language. Awesome, I didn't have to spend a couple hours converting code from VB.NET to C#!

<configuration>
    <system.web>
        <compilation>
            <codeSubDirectories>
                <add directoryName="VB_Code"/>
                <add directoryName="CS_Code"/>
            </codeSubDirectories>
        </compilation>
    </system.web>
</configuration>

Even if you don't use multiple different programming languages for your code files in the App_Code folder, you could use this feature to organize your sets of related code files into sub-folders.

Step 1: Add the following lines to the web.config

Step 2: Create a sub-folder in the App_Code folder for each language you want to support.
For Example:
/App_Code/VB_Code
/App_Code/CS_Code

Step 3: Place your VB.NET code in the VB_Code folder and place C# code in the CS_Code folder.