I would love to be able to have a common set of Classes in my root App_Code folder, which is how we are set up right now. However, it doesn't make sense to put specific code there for some application residing in a sub directory.
- Root Folder
- App_Code
- SubDirApp1
- App_Code
- SubDirApp2
- App_Code
- SubDirApp1
We currently have each production application in it's own "Root" folder with it's own application pool. Then we just mirror the main root App_Code folder there.