I’ve adjusted the manner by which I organize data in the note-taking apps I use.
A frequent method is to organize everything into a variety of hierarchical folders, noting their primary topics of concern, and then adding any sub-directory/folder organization as needed.
I’ve removed this entirely from my workflow. Instead, I use contextual keyword tags for every note. The initial thing I do now when looking for information is to perform a search, for one or more of those keywords, instead of navigating to anything.
Since I purposely do not maintain any arbitrary hierarchical structure for notes, there is no upkeep required. The act of browsing one huge directory of notes is so inefficient to attempt manually that I don’t try.
As the search within the app is lightning fast and returns instant results, that’s also irrelevant.
Upkeep of topically-relevant and logically-structured folders is a time vampire. Because of the high volume of notes I take on any given day, removing it as an element in my daily life has dramatically increased my ability to quickly make use of notes, and I’ve found that I only engage with the note-taking app when I need something (instead of blindly surfing for things).
As for the specific application I happen to use, I previously used Evernote. Like, every day. Today, due to the increasingly-bizarre adjustments Evernote has made that appear to gradually be transforming it into a homogenized project management app and social network, I’ve since switched to SimpleNote. I recommend nothing higher than SimpleNote; the sync between devices is extremely fast, and the interface remains focused on simplicity and cleanliness. It’s a solid backbone app, using simperium for content syncing.
If you’re interested in the topic of how changing the interface of something to be goal-based instead of discovery-based can improve your workflow, I highly recommend this podcast series, which distills the ideas into small, actionable steps.