On the other hand, it requires the user to read minds and figure out how the developer might have classified the application. If I'm looking for After Effects, should I look under Graphics or Multimedia? Or maybe Utilities?
I agree that using Company Name as the top level folder might be the worst option. If I'm looking for some random utility app I downloaded and installed, why should I have to first remember what the name of the company was who made it?
First the categories need be a bit more distinct. Also, a program might be allowed in more than one category. In a commercial case I could see stupid companies stuffing their app in as many menus as possible.