I am getting the following error when I put class files in subfolders of my App_Code folder:
errorCS0246: The type or namespace name \'MyClassName\' could not be fou
In Visual Studio (2010 at least, but I recall past versions too), you can right click on the folder, within Solution Explorer, and then choose "Include in Project".
Then on the properties tab for each file (or select them all at once), you choose "Compile" for the "Build Action" property.
This worked for me.