>1) Is it better to use an INI file or the registry for keeping certain settings and why is that particular method better?

Standard programmer's answer: it depends. Registry is local to the computer and/or user. Ini files are local to the application and the settings there can be shared among users. You can also create ini files for each user, and not by machine where they sit, but by username they use in the app. So their settings follow them wherever they log in.

So depending on what you need, you use what fits.

>2) Is it better to have all your program is one project or is it better to have each section in a seperate application that is eventually linked to the main project and what is that particular method better?

For a project big enough that having everything in a single project would be a hassle, and where logical subsections exist, which can function on their own, yes. Otherwise, waste of effort.

>3) Is it better to keep all your files in one folder, or should you have sub folders for forms, menus, reports etc?

Definitely separate subdirectories. You know where your things are, and find them faster.