My favorite tools for this sort of thing have been TiddlyWiki as well as Scribble (Racket language). An essential feature present in both is that they both are

My favorite tools for this sort of thing have been TiddlyWiki as well as Scribble (Racket language). An essential feature present in both is that they both are incredibly hackable and customizeable since most products don't support enough organization for me. However, my main complaint with these tools is that while they are customizeable, it is sometimes nice to have a WYSIWIG since some notes I take will only every be looked at as I am writing them so having instant feedback is nice, even if the resulting document is imperfect.