I write everything with a pen and paper. it's more free-flowing in the moment for whatever I am working on. For me it's more important to get the idea out of my head and worry about storage/lookup later. I have a dozen scrap pages with half-baked notes.

Later on I'll transcribe them into text files or other media. This is where I might do some cleanup work, expand my thinking, add references, etc. Sometimes they become full blown essays. These get archived so I can dispose of the scrap pages. These might expand later as I work through other notes or ideas.

I primarily use text files because they are portable and every editor can open them. Occasionally I'll use image files for illustrations or complicated spacial notes. The big idea is they are easy to store and use, but sacrifice some of the cooler note taking features others have offered.