I treat my notes as if they were a software project, which is to say, a collection of text files organized according to domain-specific methods. I use a code editor to write and edit notes (Textmate in my case) -- this has the bonus of not just using my familiarity with my code editor, but it actually adds to the value of improving my skills with the code editor, since that makes me better at notes and at code.
I keep two projects -- "life" notes and "work" notes. They are stored in Dropbox (and are additionally put in version control, although I commit changes rarely). Storing them in dropbox makes them all accessible on my mobile phone, which is nice.
In the root directory of my "life" notes, I have:
a few scratchpad_{identifier}.txt files (alpha, beta, etc.) -- so I always have an easy file to jump to to take notes on anything. I then synthesize these notes into a more useful location.
todo.txt -- a todo list schedule.txt -- notes on my schedule (typically to aid planning things a few weeks ahead, not a replacement for a calendar app) goals.txt -- keep my life goals front and center
and then directories, which included .txt files related to their title, or further subdirectories:
career culture (notes on articles) finances identification (keep track of useful info like VIN #) journal knowledge (non-career related learning) lifestyle (hobby-related notes, fun ideas) media_lists (books to read, books read, movies (watched/to watch), podcasts, etc.) projects (personal software project notes, ideas, before they deserve their own repo) travel self_improvement writing
Like a software project, I sometimes "refactor" the notes; the goal being to improve the ease of storing and the value of retrieval of the notes -- as a bonus, going through the notes refreshes valuable information for me.
My work notes are organized in a similar manner, but related to work things.
It's an awesome workflow -- almost everything I write starts in a scratchpad, and either gets migrated and synthesized elsewhere, or (like code) deleted if not worth maintaining.
After a lot of exploring solutions, returning to the core concept of files in folders and a text editor has been a perfect fit for me -- I never used to be big on notes, now I relish it.