TiddlyWiki
TiddlyWiki might be the best software I discovered in the past ten years. It might seem nerdy and hard to understand, but trust me, every bit of it is worth it. It was exactly what I wanted five years ago. And don't be fooled by its simplicity.
It's highly customizable and over the last years it has kept running stable, getting better and simpler to use. By now there is even a free online hosting service.
If there is something like love in the world of software, it's spelled Open Source. If there is someone like Jesus in the world of software, his name is Jeremy Ruston. (I hope nobody will crucify him though.)
Over the past years I've also built my own extended TiddlyWiki instance and as with anything, the main challenge is to keep making the best use of it.
I'm currently hosting it on GitHub and if you're curious about it, just send me a message and I'll give you access so you can see what I'm fuzzing about.
Update: Tiddlyhost works perfectly fine. A lot simpler than GitHub pages to be honest. I might just switch.