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I loooooooove (one O was not enough to express) Evernote, however, one significant deficiency is that it only supports one level of directory categorization (Notebook->note) instead of multiple, like a directory structure. I contacted them about this but they said they didn't plan on implementing that feature.

As a result, the classification of my notes is too simple and insufficiently indexed in an only one-level hierarchy.

The question here is: is there another web/mobile app which is just like Evernote but supports a multiple level hierarchy of notes?

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The standard answer here is that I, like others, haven't experienced a condition where tags and tag intersections aren't at least as powerful as folders. It just takes getting used to. Assuming you disagree, then perhaps OneNote? There are many, many other tools for this...what OS are you using? Do you need mobile support? – Chris Dec 5 '12 at 1:23
Yes, mobile and web, both. OS-independent – amphibient Dec 5 '12 at 1:53

Evernote does support notebook stacks, at least on all the platforms I use (iOS, Android, Windows). That provides one additional layer of hierarchy.

I've found (like Chris in the post comment) that tags are more powerful. The stumbling block I had to overcome was not using enough tags. One tag on a note isn't enough! Lots of tags, with a little thought to how you create them, and Evernote's saved searches work much better for me than a notebook hierarchy ever could.

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I use DevonThink extensively on my Mac because I need a highly-structured way to organize my notes. It is very powerful and reliable software.

Their iOS app, DevonThink to Go, is fairly new and still may need some ironing out, but it may be worth considering now if you just need a mobile solution and aren't dependent yet on sync.

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+1 Devon Think is a great app. I'm also using it for managing and categorizing large amounts of data. – MostlyHarmless Jan 10 '13 at 20:47

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