WORK: I don’t a defined organizational system since it hasn't provided value for me, but my general guideline is to store the notes nearby the context of the associated topic. This can be in project file folder, on a white board, or in a collaboration tool wiki. my formats are usually txt files, email, paper (notebook, paper), or onenote. Often times I will write a note on a scrap piece of paper just to remember a topic better.
PERSONAL - I also always switch but Evernote has worked for the last year. here is my sample setup (although I do not swear by it similar to my work structure). I don’t like post-it notes near my home rig ; ). Here is a snapshot: https://www.dropbox.com/s/tlnzut54agbycnh/notes_screenshot_f...
I found this resource very helpful when building a solution for handling multiple sub-tasks in a todo application (started with adjacency and ended with closure based on recommendations). I'm assuming this issue is limiting some of the existing software to prevent 1:n functionality. I also discovered postgres has built functionality to support tree structure so might want to investigate if you are exploring options https://www.postgresql.org/docs/9.2/static/ltree.html.
PERSONAL - I also always switch but Evernote has worked for the last year. here is my sample setup (although I do not swear by it similar to my work structure). I don’t like post-it notes near my home rig ; ). Here is a snapshot: https://www.dropbox.com/s/tlnzut54agbycnh/notes_screenshot_f...