I would also guess that how helpful people find these programs is based on how you write--folders for all these different things? Why?
I guess it depends on how you write and what you write.
I find it extremely helpful because, while writing anything in my WIP, I often also have asides, notes and thoughts on all kinds of things: plot, characters, etc.
With Word, I would also have numerous versions of the same document (saving to a new appended doc every time I made substantial changes) and would have a little trouble finding an earlier version if I wanted to check something or extract something. (A common problem with Word is that the preview feature is broken so I would inevitably have to open numerous documents and check each one.)
But anyway, back to your question: I find the use of folders invaluable. I have folders for each section of the story, broken down into scenes and some scenes are broken down further into notes for the scene as well as relevant thoughts.
I have a folder for research (that includes links and photos) and a folder for characters, broken down into documents for each character and subdocuments for anything else like interviews, photos, characteristics, dialogue snippets etc.
I get a lot of WIP specific ideas not pertinent to the specific scene I'm writing (future plot points, possible conflicts, possible characters, unattributed dialogue snippets, possible endings, possible beginnings, observations, etc.) and have relevant folders I can quickly jot them into.
I also get ideas while I'm writing (or musing) about blurbs, synopses, elevator pitches, etc that I jot into the relevant folder when they strike.
It's handy as hell to have all that there, easily visible and accessible - as opposed to how it used to be when I used Word and these snippets and thoughts were scattered throughout my writing folder (and sometimes throughout my hard drive!)
So, for me, the folders are an invaluable and necessary organizational tool.