This looks like a good thread to revive
I'm very interested in how other people organise their stuff, especially how you combine 'what to do' with 'how to do it'.
I got myself into a lovely mess with the tree over the past few years: lots of information tucked away I'd entirely forgotten was there. After spending a couple of hours moving things to the right places, and then moving them again when I thought of another level of organisation... I realised I need a different system.
Here's what I'm planning to do -
1) Use user-defined keywords (ctrl+k) to 'tag' everything related to (eg) product development. (You can select multiple items and allocate the same keyword to them all at once - useful if you already have them more-or-less organised in folders.)
2) Create a search on user-defined keywords only (that's a checkbox at the bottom of the search page) for 'product development'
3) Lock this search and copy it to the overall 'projects' folder.
Now every time I add a new note, journal entry, idea, task, web page etc related to product development I remember to 'keyword' it as such. And then no matter where I dump it in the tree, it'll show up in the saved search folder in the right place.
I'll do the same, of course, for product development > membership site and product development > membership site > Amember, and build a new 'tree' of searches. So I can still have a visual view of the hierarchy, which I like, but I don't have to worry about losing things because I forgot to store them in the right folder.
Instead I just have to worry about remembering to tag things...
Of course saved searches can do more than just replace or supplement a static folder structure. I can just as well save one for 'all membership site tasks due in the next two weeks' or 'all I Ching readings about membership site development'.
Oh, Kinook...? This leads to a feature suggestion/ question. Would it work for search results to appear not just in the search results pane, but also in the tree as virtual child items of the search? It'd make it easier to browse their contents in a full-size window without losing site of all the results. And it'd turn saved searches into 'smart folders'.