dl__

I haven't found the perfect solution either, which is why I still play with evernote and one note and others. I guess my most used note taking program is WinOrganizer but it's winows only and its not free. It does allow me to create note hierarchies and link notes to each other. It doesn't have the ubiquitous capture and syncing of evernote but at least for synching you can get part way there using dropbox or windows live sync to keep the datafile synched across computers. I'd like to drop winorganizer for evernote (or one note) but I find the flat list of notes doesn't work for me long ter

I think inherited tags allow you to do the same thing as sub-notebooks and more. Tags are more flexible than sub-notebooks because they can handle classifications that are not hierarchical as well hierarchical classifications. Sub-notebooks can only handle hierarchical classifications.

If you clip using the firefox scriptlet you can specify the tags at clipping time.

They seem to be unwilling to view notes as anything to be a collection of flat lists. I'd like to vote for a real tag hierarchy as well.

I had exactly the same reaction. Letting you structure the tags so they display in a hierarchical manner when they don't actually behave in anyway other than flat was very confusing - and disappointing. I hardly bother with tagging in evernote as a result. When I have notes that need to be structured, I move them out of evernote.