Like others, I've wished for the ability to have deeper hierarchy of notes. I have to think harder about using tags to achieve this; it just hasn't been a "natural" approach for me. For those looking for an alternative, check out PersonalBrain - http://www.thebrain.com/products/personalbrain/. Actually, I'm a heavy user of both apps, so maybe alternative isn't the right word. Frankly, I've been struggling with how to either 1) create a workflow leveraging both apps or 2) settle on one over the other. I don't have the inclination to go into a detailed comparison of the two atm, but here are a few top of mind thoughts... What I like about PersonalBrain is that it allows me to be more organized (with parent / child hierarchical relationships). What's nice, though, is that you can have multiple parents for any though, so it's much more powerful than the traditional folder structure people are used to. You can also have "jump" thoughts to connect one thought to another ("sideways") without making either one a parent or child to the other. PB also allows you to assign both multiple tags AND thought types to any thought. It's incredibly flexible. What I've been trying most recently is to use EN as the initial repository, dumping everything into it. And then seeing if how it works to put what I think is the more powerful PB interface on top of it: i.e., copying EN hyperlinks and pasting them into PB. Ideally, though, I would just use one app to reduce the amount of time spent organizing data. It sometimes feels like I'm doing double the work. While PB lets you publish your brains to the cloud, this means I need to have connectivity in order to access. I appreciate that I can store notebooks locally with EN and access them from anywhere regardless of whether I'm connected. Anyway, if you haven't checked out PB, I would encourage you to do so. There's a free version. I think it will give you some interesting thoughts (no pun intended) on how you organize your data. Perhaps when I have more time, I'll show some examples of how I would tackle the same activity in either app... and what I see as the pros and cons of each for my own usage. Any other joint PB and EN users out there? I would definitely like to hear how you're managing the relationship between the two apps.