Hi,
I just came across this and would like to add some comments.  I use ndxCards regularly now and own a few other note taking programs as well.  I have settled on ndxCards ( I do use OneNote when I want to keep my scribbles as scribbles ) for the most part & would like to share why I settled on it.

Note taking programs should not constrain a person while taking notes as to how they organize the note - when I take a note, I want to do just that.  I may want to tag that note with some keywords - but then again, I may not know how to tag it at that time & will come back to it later.  Most tree-based programs fail in this regard - while I can 'park' the note in some general category, somehow, the note does not seem to stand alone as it should.  After all, I used to note cards & post-its in the paper medium & not note-books with subject tabs that forced you to flip to the right page before I can take the note.

Often I want to know where my note came from - I want to be able to jot down the magazine or book which was the source of my thought/note &  perhaps go to it later, or even give the reference to someone.  I like the Source card in ndxCards, though I don't need all the reference citation formats that the software offers.

Not all of my notes stand-alone, nor do they fit in only one category.  So I want it to be part of a structure as well. ndxCards allows me to use both the keyword system and the tree-structure system.  I have several outlines which are just tree-structures for my notes.  As you said in the previous post, the tree structure offers benefits of seeing a visual collection of a set of notes.

I take notes because I want to use it later.  I like that fact that I can just drag drop notes from ndxCards into my Visio diagram, or create a quick PowerPoint presentation directly from my outline.  Even with my OneNote, I am left with copy/pasting from various part of my 'notebook'.

None of this is to try and change your review - just thought I would share my view of 'note-taking' programs.