I tend to just scribble in Vim though, or use paper and pencil.
I find it to be sort of halfway between Notational Velocity and Evernote. Like nv it stores everything as flat files, but like Evernote you can add some structure to how your organize things.
The nice thing is that Zim uses plain .txt files without the need of a database. So you can also view and edit your notes/pages using any text editor instead of Zim itself. Making backups is also very easy this way.
I keep these text files in sync across my devices using owncloud. That way I can also use it on my smartphone by just viewing the plain text. No extra apps necessary.