OP said he wanted an open source solution. Other than that, I can find no faults in using Evernote for this purpose. I use it for my personal stuff.

Where Evernote falls down, and this is by design according to CEO Phil Libin, is in sharing across many people. Libin says Evernote is not social, it's anti-social. As such, it doesn't work when you need to collaborate on notes. But see Evernote Business which seems to contradict this assertion.

OP was talking about a personal solution so the social aspect doesn't apply.

Working within the editor. As a save and reference Evernote is great but for working within the document its awful. Just try to add/remove columns in a table or rearrange photos within a note.

How about the new OneNote for OSX?

Doesn't work for confidential data.