I'm also curious as to Evernote alternatives. One of the features they cut a while back is the ability to have nested notebooks and notes, a feature I loved dearly, but was cut several versions ago. I know some people who are still on the very first versions of Evernote due to this feature. There are other features that try to compensate for this (tags, keywords, etc), but I'm looking for genuine hierarchy of notes.
My main intention is for cataloguing, studying, and understanding many deeper contexts in religious studies.