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 term. If I have notes that I need to refer to frequently over time I want to put them somewhere where I know where they'll be - not watch it drop further and further into history, only recallable by some search. The search doesn't work because over time, as my notebooks grow, searches bring back more and more hits. One note is pretty cool but its hierarchy only goes so deep (notebooks - tabs and pages) and although it is apparently built to sync they do not provide a syncpoint for all one note users. You have to have a shared folder or webdav host. So I keep hoping some one program will combine the features I really want: easy capture, sync and organization so I can drop all these other ones. But now, thanks to you, my problem has gotten worse because I have to check out Zotero now...

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.