I think a note-taking system is the type of application that is so close to your mind and so personal that it should evolve with you. For the past two years I've been using my own streamlined/lightweight application. It has a minimalist UI (basically a tree view outliner and a rich text box), a reduced feature set, it is maintenance free, and it grows with me. It is full of personal conventions, shortcuts and whatnot. When I don't have access to it I feel a piece of my brain is missing.
You start developing a system to organize, then you fine-tune it, you find patterns in your own notes and you "officialize" them, turning them into first class organization atoms. When you do that for long enough, it completely diverges from any other persons systems.