What is the best way to organize the files in your project?
For example do you put all user controls in a separate folder or do you place them in a sub folder? Do you h
First the purpose of folder separation is to be an extra level of documentation, to let the programmers find code easier. That means you should not have extra levels "just to organize stuff". That excludes folders named Classes, Controls, etc.
Some examples:
If you work on a thee tier App it would make a lot of sense to have something like:
Project\Tier (Model|Controller|etc)\Classname
If you program is big to the point of having separate functional areas I would go with:
Project\Functional Area\Tier (Model|Controller|etc)\Classname
That is particularly usefull when sub-teams work on the different functional areas.
Also refrain from very deep folder trees (IMHO, more than depth 4 is too much) and keep your folder names compact. Some tools might have limitations on path size as low as 255 chars, so this is one place where brevity has its place.