I stumble more and more on the note taking question, with consequent implications :
Questions never quite answered, always reflectiong on the matter, learning what you want to learn. On this page I will write about the different tools I used, namely : OneNote, Google keep, Notion, Obsidian (more broadly .md files), notebooks. Then I'll explain how I use them.
My need are probably not the same as everyone, my bias are :I used OneNote from Microsoft (boohing) for some time (4/5 years), it's the tool my father use, but it's not my cup of tea. The spacial way of organizing stuff is really interesting, especially for writing papers, comping data from multiple pdf and notes. But it is quite heavy, your file are stored on your one drive (which is sometimes hard to find). It require a Microsoft account. The folder system is rather strange: virtual notebook contain tab that contain pages, old skeumorphism that doesn't make much sense nowadays. UX side note : the toolbar is a bit bloated, equation are not easy to use.
Have used it for few month, I like the colors and the way note are displayed.
Notion is a wonderful tool, nice color selection, I love it's UI, you can embed wathever you want in the page by a drag and drop, etc...
but.In many ways it's exacly what I don't want. No way of truly offline syncing files, everything is stored on their servers. The app is really laggy, and I'm not to fond of browser app in general. They have their own file format and exporting form notion to obsidian has been a pain in the ass. Don't get me wrong, it took maybe 2 hours, but only because a nice person had made a renaming script beforehand, and even then, it should have been way easier.
Markdown files are probably the way to go for long lasting notes, there seems to be infinite ressources of markdown editors. I like Obsidian because of the way it displays Markdown, all symbols are hidden and appear when the cursor goes over it for editing. It doesn't need the dual preview pane that is common in markdown software. Graph view and all other advanced niceties, I gotta say I don't really use them. There's not much colors (also it can be added with plug-ins), but good integration of pictures, latex equation. It can also contain pdf and epub in it's folder and split pane with a note. It's quite versatile, all my markdown file are stored locally and backed up regularly with the rest of my computer.
I sometimes use Visual Studio Code to edit my markdown when working on a code project, in order to avoid app switching. I don't use preview, reading markdown as is, syntax highlighting can be quite pretty with the right theme.
Tables can be impractical, as can be media in general, but I don't use those a lot in this kind of context.
Been using notebooks for a long time, but scarcely, for some poem / lyrics and thought. I started using them a lot more recently, mostly to develop my project ideas, as a reflection support. At the end of the notebook I keep all the utility stuff : index, to-do, ideas on post-its that want I to develop further in the notebook. I made some symbols so I quickly know what a page is about in the index, I use color-coded post-it to mark the pages I may want to come back to.
The blog has a particular status in all of this, it's made to readable by someone else, there is a kind of "quality standard". It's an interesting place to develop idea, writing a bit more in depth than I would in other mediums. It's also a place where I store methodology, how I did something. Thinking it for someone I don't know ensure that a future me would be able to understand. A blog also give a form of finality, for exemple, this very page gives me a sense of "ok, this idea has been researched, my brain can go search stuff elsewhere".
Depending on the information, I don't use the same tool, it really comes down to how and if I really want to remember it. It's mostly a question of feeling, for me markdown is this kind of "always present" thing, where notebook give you the opportunity to forget, maybe revisit this space later. I think it's because file can always be rewrote, reorganized. Notebooks are fixed, ink is dry and now it's read-only.
As a tl;dr :