Working with subdirectories to classify apps on iTunes I have many apps on iTunes, some installed permanently onto the iPhone, some others not installed, and same thing for iPad. 

I'd like to separate them on the computer (Windows 7) to be able to make targetted backups. So I'd like to put them in some subdirs : "iPhone/Permanent", "iphone/occasional", "iPad/permanent", "universal/occasional", ...

Can this be done without breaking iTunes ?
That depends on what else you use iTunes for.  You can turn off the "automatically sort iTunes content" switch, which will allow you to spread files all over the shop, but be aware that fresh downloads, iphone purchase transfers, updates, and all sorts else may not honour your choice when doing updates and the like, resulting in potentially multiple versions of multiple apps in multiple locations, and also having potentially adverse affects on your other iTunes content such as music etc.

I'm not sure about the Windows 7 aspect of this next bit, but on Mac you could "label" your files into categories, and then make a smart fodler that searches out for apps in location X (default) with Label Y etc - I think Windows must have some similar tagging system, certainly it can handle the saved searches/smart folder equivalent ably enough to approximate the same behaviour.