In order of descendance, I prefer to:
write down by hand → type on physical keyboard → type on virtual keyboard
I used to have physical notebooks to write things down in. Loved the idea, never stuck with the process: too slow, can't do much on the go¹, can't do it with one hand.
¹ I often take long walks around town, which is when I get a lot of good ideas
Nowadays, I spend a lot of time behind the table, at home. The table is wide enough to comfortably host the laptop and a wide² yellow sticky paper stack. If I have a quick idea and am near the table, I would write it down on a sticky, take it off the stack, and stick it to the top of the table, by the stickies.
² I find wide stickies better for writing and/or jotting down quick design
For outlining and quickly jotting down a complex idea – a character, a description of a design – or a list of ideas I use [Indigrid](https://innovationdilation.com/). It's a quick, minimalist outliner ready for full-keyboard control, developed by a friend of mine. There, I have several categories for long-term items I keep track of:
* writing (plot, characters, details etc.)
* worldbuilding
* web game design
* forum RPGs planning
* major projects
* non-fiction books
* various notes (eating & dieting, songs of the year etc.) & ideas
* thoughts (things that crop up on my mind)
* questions (things about life I want to find the answer to)
For to-do, I use [Dynalist](http://dynalist.io). It's slow for my taste³, but the workflow is very useful for my kind of tracking: mostly-linear, mostly-checkbox, what-to-do and what-needs-doing. I've also been looking into moving to [Notion](http://notion.so), which is equally slow to load⁴, but provides a wider range of functions – something I find myself needing sometimes, when the thoughts move beyond linear structures.
³ it takes several seconds to load, so I keep it open constantly
⁴ both Notion and Dynalist being Electron-based apps, which takes very long to load for such small apps
I take the iPhone wherever I go, so it seemed appropriate to find a notetaking app for it as well. I scribe down ideas on the go, one-handed, onto Better (which is a bitch to find now; its icon is a yellow square sticky; no clue if there's an Android app). My criteria were:
* quick to access,
* simple design,
* easy to write things down
Better satisfies all three. It's like Google Keep, only even slicker-looking and fast.
I used to use Google Keep for on-laptop notetaking. It proved to be too slow, though I'd used it for a while and had accumulated a sizable stack of disparate notes.
I'd also used OneNote for a long time, and it was okay. I did, however, find myself having to navigate what ends up a maze of notes when you're in a hurry to jot one down, so I didn't stick. Evernote was no good, either, for similar reasons. (Notable, a notetaking app trending on GitHub for the last week, is like Evernote, but slicker, so if you like Evernote, check it out.)
Long texts – like published worldbuilding – I write in Markdown, in [Caret Editor](https://caret.io/). It's simple, straightforward, a bit slow (Electron, eh), but exactly what I want from a .MD editor otherwise. I love that it uses inline Markdown highlighting⁵ – it fits my mental model of a Markdown document well. It's effectively free-to-use, as long as you can tolerate the pop-up that asks you to buy the license. [Beta releases](https://github.com/careteditor/releases-beta/releases) – stable as a hyppo, far as I can tell – are free, though.
⁵ if you wrap some text in asterisks, it becomes oblique while still showing the surrounding asterisks, and so on
For life stuff, I have plain-text files for written stuff (journalling, dream-logging, quotes, and some scattered thoughts) and a big, overarching Excel table (tracking: habits, weight, exercise, finances).
Overall, I use Notepad for cases where I need to write down a thought quickly. My main criterium is ease of use, centered around swiftness of response. Notepad is the quickest so far, with Indigrid close second.
On a related note: there was a mention of a guy with a brilliant, if sophisticated, method of notetaking on a podcast (could be Wireframe). He's carried around glasses with an in-built projector (a la Google Glass, but hand-made), and a one-hand keyboard. When he had a thought to write down, he'd switch the whole device on (no idea how, exactly) and type it down. When he needed to find a previous note, he'd switch modes and type out the text he's searching for. It's been a while for him and his experiment, so he has a lot of notes stored – about people, about fields of science, about himself etc.
I'd love something like that. Even typing – I type quickly – is slow, and I don't like the sound of my voice enough to tape it. If I ever get an advanced prosthetic arm, I could program it so, after a certain gesture, it would react to "muscle" movement for keypresses, and store text either on a connected device or internally, and project the results onto a lens⁶, so I could see what I'm typing.
⁶ I mean, I'm already assuming being able to program a prosthetic arm for use as a keyboard, so of course it's gonna connect to digital lenses wirelessly.
Alternatively, AR keyboard on my biological arm.