I have been using TiddlyWiki to organize many of my notes since late 2006. Yet many people have never heard of this wonderful tool.

TiddlyWiki is a webpage file (an html file) that has been stuffed to the gills with code, converting it into a one file database for notecards, called tiddlers (tiddlers is a British term for a small fish, like a minnow) you create in it. The tiddlers are connected to each other by tags and hyperlinks you add to them.

TiddlyWiki is infinitely customizable, with a growing toolbox of plugins, macros, filters and other features. You can create your own visual stylesheet for your TiddlyWiki, and enhance its appearance and functioning in ways too numerous to count here. Here is a screen shot of a visual theme I use in my TiddlyWikis:

You can embed images and video in tiddlers, create tables, tabs and iframes, and even draw pictures and scrawl hand written notes in them.

TiddlyWiki is Open Source, meaning it is completely free. You can download a separate empty TiddlyWiki for each subject you want to take notes on. Take that, Evernote!