+1 for Zim, even if you don't much like wikis. You don't actually have to use wiki markup or anything with Zim if you don't want to. You can just organize thing

+1 for Zim, even if you don't much like wikis. You don't actually have to use wiki markup or anything with Zim if you don't want to. You can just organize things with folders, subfolders and tags and never worry about creating links. 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.