I don't have a good answer to your question, but I have a few loose thoughts. One panel, not two (or three). OK, you'll always want something on the side, such as a place to store attachments, but make it optional.-tranglos
That sounds a bit like EverNote, where you can make the timeline and tags panels fly out with a hotkey. But I suspect you mean something more fundamental than that.
As soon as you have two panels, you must decide what the TAB key does: does it navigate panels, or does it insert a tab?-tranglos
Unless maybe you choose that default note status is Locked, and have to press an extra key to Unlock it for editing?
while a flat, tagged list makes that problem go away just like that. -tranglos
Which NoteFrog has. I was rather surprised to see a "one dimensional" notekeeper appear, after years of two-pane dominance.
Evernote [...] I am sure it's not the end of the road, and someone will come up with an even more ingenious design - but I worry it will be on the web, where all the ingenuity is gagged and hampered by all the inconveniences and all the dangers of living inside a browser and in the cloud.-tranglos
I bought Evernote with my own money, though I used it mainly at work (at the time). Whether it had been my money or the company's, I would not have accepted a cloud application. I would feel that data I had laboriously accumulated was being held hostage to my or the company's continued subscription fees. That seems an absurdly bad business decision.
As for the good old tree, I want it infinitely malleable. The manually imposed hierarchy is fine, but also let me be free from that. Let me show the tree as a filtered flat list. Or let the tree arrange itself automatically according to rules, e.g. group items by date (years at the top level, then months, then maybe days, whatever). Group by tags, by content, by all kinds of properties and metadata.-tranglos
And
that sounds a little like the filtering and virtual folders of
The Bat!, or the rather similar ideas IainB has been wanting mouser to add to CHS.
I did register Right Note Pro today after all, because I like it more and more.-tranglos
It must be good

but when I need to jot down just a phone number of just a URL, where do I put it? It's too small to deserve a branch of its own in KeyNote, but if I put it in a note together with other stuff it gets lost in there, and pretty soon I have a single note with years' worth of tiny little bits like that. Soon I have no idea what that URL was for.
I have a big catch-all note like that in KeyNote. [...] wait, wasn't I suppose to organize stuff?-tranglos
Part of the problem is the discipline needed to add meaningful details, but discipline isn't the whole story. If you're really busy, you don't always have time.
For things like your examples, when I was dabbling with Black Hole Organizer, I mostly put them in their own notes, but made the first note in the list a catch-all that had internal hyperlinks to the individual ones. That worked reasonably well for a small number of things I frequently needed rapid access to, but could scarcely be described as "organised."
I guess it all boils down to how hard it is to organize dis-organized stuff, and we accumulate so much of it it's not even funny!-tranglos
I keep remembering what I think was zridling's motivation for moving to Linux; an unwillingness to commit more and more information to proprietary formats, and an intent to keep it in plain text files. For me, a Windows-based alternative might be everything in plain text files, and running Archivarius more often. I just want to save and retrieve information. I don't need to impose structure on it, at least, not in the sense of making an printer-ready report. It then depends on what you find the easiest way to search, and you have this tension between live search maybe with tags, versus tree organisation. That's full circle; no clear resolution of this issue yet...