I think I get what you're saying about OneNote, Azayzel, when I first heard of it (after installing Office '07) I didn't think it would be much use to me either. I haven't looked at the '03 version, so I don't know how different it is or isn't
After playing with it a bit & running through the "what the heck is this OneNote thing" tutorial, I started to see possibilities for using it to organize my projects at work, and I wish that it had been around when my wife started her dissertation, as I think it would have made a lot of the stuff she's doing a lot easier (she's too close to the end to bother with starting a new method, but the one she uses now is much more cumbersome than I think OneNote would have been for her).
It also offers a workable way for her to grade papers electronically when she starts teaching again this fall. She can accept e-copies of the papers load them into OneNote as images, make her comments and mark the grades and then send the whole shebang back to each student as an XML file, while keeping copies of the paper and her notes -- something that most teachers/professors would love to be able to do -- all without ever printing a single page. On top of that, the notebooks, sections, and pages pretty much organize themselves into a gradebook file for each class, student and assignment, respectively.
I think the primary advantage over using Word to do the same things is the way that OneNote allows organizing things -- Notebooks containing sections containing pages, and you can add/remove and move around any and all of those elements with excruciating ease allowing for more free-form sorting than Word can handle. It also handles storing and retrieving (to and from the hard-drive, I mean) the stuff you put into it for you, so you don't have to hunt for it, just open OneNote, and there are your project notebooks. The only time you have to worry about where something gets put is when you want to close a project or re-open one that you've closed, between sessions, it holds onto your open projects and keeps them right there handy.
Then, of course, there's the way it allows easy searching of both 'ink' text, and text inside pictures. We had a short (under 100 pages), very old (mid-1800's) book that my wife needed for her research, that she could only have for a couple of days, so we photographed the pages and sent it on back. With OneNote we can toss those photographs into a Notebook and she can search the contents.
I'm not trying to push OneNote, though I'll admit to being a bit excited about it lately (since it's new to me), and I'll further admit that I haven't had all
that much time working with it, so take my opinions salted to taste (as always). I'm just trying to explain the potential usefulness I've found and see in it.
Naturally, not every tool is for every person, so whatever works for you works for you, and that's that. Like I said, I'm not trying to convince, only explain.
