Sorry, if it not right place to sharing this. Currently I'm working on software that helps easily organize notes using nice nested structure. If someone interested please check it here - http://unit.ms/
I also have the same issue. I love tags, but in lot of cases I need only one hierarchy dimension, something like folders on pc/mac. 2 levels deep in EV (notebooks, stacks) is not enough for me. The best what I found is to create my own software. If you are interested please follow this link - http://unit.ms. Would be happy if it could solve your problem also.