My team is creating an application that has a single entry point. There will be a single entry point, meaning only one item on the Windows 7 start menu/Windows 8 start screen. Other than "that's how it is done", can anyone explain why users would benefit from placing this one item a folder? I say that going directly under "All programs" makes it faster to access for users who don't search or use the desktop to start applications.
As far as I'm concerned, putting single entry points into folders is just annoying. However, if I have multiple program entry points and they can be categorised, I'd put them in folders. But that's just my preference.
To be frank: users will put things wherever the f*** they want. I know people who OCD-style categorise everything and would put your entry point in two hunderd layers of folders. I also know people who don't give two s**ts where their programs are.
The point being, as a developer it is irrelevant to you where users put their icons, as long as they can get at them. However, you might want to know what your users find most useful so you can install it there to start with. I can only say 'do some research' to that: every group of users is different, so talk to yours and find our what they like.