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