For me the best methodology can be abstracted to the following 3 things and in the end of the day is all I really need:

    1. Ability for a tree-like organization of notes. It can be as simple as some directories in your OS with text files and subdirectories. Or a cool app with Notebooks and Sub-notebooks etc. It doesn't matter.

    2. Ability to search everything at once. It can be a grep command or a an app with text search functionality. It doesn't matter again. Strive to have easily searchable titles and content in the notes (What "easily" means here, depends on your search preferences and habits).

    3. Ability to effortlessly synchronize your notes to different hosts. Maybe you'll put your simple directories and subdirectories of text files in Dropbox or something. Maybe you'll use a paid or open-source application with a mobile app or a web client etc.

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I explain the thought process here https://news.ycombinator.com/item?id=31799695 but it isn't important as those basic rules above.