One senior researcher I know, though an extremely early user of computers and Emacs, still uses basic paper notebooks for writing things down. The system is not searchable, not hyperlinked - but he still finds things almost effortlessly even though he hasn't been young for a long time.

So if the only habit that sticks is Apple notes - keep doing that. At least in my experience hyperlinking was never that useful, because the act of remembering what to hyperlink where was about as difficult as just remembering the what other notes exist - in which case, what do I need hyperlinking for? I also find hyperlinked text hard to read because you end up in Wikipedia style 3 pages deep hyperlink hell - a fun way to spend an afternoon, a terrible way to work and understand.

The act of physically writing things down commits the event to incidental memory. The more effort it took to concert all your neurons into outputting an action, the less easily it fades from your impression.

I find with physical objects I can better remember where it was spatially. I know that note was about 3/4 of the way through the green notebook, on the right-side of the spread, near the bottom of the page. Or something to that effect. I find the same thing with physical books over ebooks.

I use Obsidian for two reasons - I'm across OSs and I like it as plain files. That said, the Apple Notes UX (especially search) is absolutely incredible. If I was all Apple, I'd use it in a heart beat

I really appreciate the replies, thanks :)

It has helped me make some sense of it all.

My solution is to make various capture methods. I use Apple Notes for personal notes and Obsidian at work.

With Apple Notes, I used the Shortcuts app to append some text with a timestamp to a note where I log those random thoughts. I use this shortcut on my phone to type stuff, I use it with Siri via CarPlay to capture stuff while driving, and it works decently well. I have a list in Reminders I can easily throw stuff into as well, via Siri or whatever else. It looks like iOS 26 will make some of this better as well.

With Obsidian, I do something similar. I currently also do it with Shortcuts, but have made similar solutions in bash, Hammerspoon (lua), and AppleScript. I have a daily note in Obsidian, and while I always have that open, I also have a keyboard shortcut (and desktop widget) where I can quickly bring up a text prompt, write something, and have it go into my daily note (or a shared log like I do with Apple Notes). I mostly use this to keep track of what I actually did each day so I have a record of it. I need that to be low friction or I won't do it.

It actually works a little better with Obsidian, because it's simply appending to a text file, so I can use markdown really easily to format things. I'm hoping the better markdown support in Tahoe will allow for me to add some better formatting to Apple Notes. Shortcuts has a markdown to rich text converter in it already, but it didn't work for what I was trying to do (or I did something wrong). Shortcuts has a way to add to a list in Apple Notes, so that way can look a little cleaner than raw text, given there is no formatting. I swear I got formatting to work once before, but I deleted the Shortcut, so I don't know... maybe it was in Obsidian and I migrated the note back to Apple... I spent way too long messing with it.

Apple Notes also has various other capture methods, live OCR from the cameras, speech to text, etc. I don't use this that often, but I try to remember they exist for when they would be useful.

I've gone back and forth between Apple Notes and Obsidian for personal notes, and I've told myself I'm going to stop this. The draw of Obsidian is having plain text notes that are effectively future proof. However, dealing with media is very annoying. I don't have a lot of images in my notes, but with Apple Notes it's easy to just drop something in (and I can search/copy text in the images). With Obsidian I usually end up trying to distill whatever information was in the image into text, so I can search it, and I also don't have to deal with coming up with a system to manage how and where images are stored, so they can be referenced, that won't be a nightmare in the future. These are things I don't need to think about in Apple Notes.

If Apple Notes works for you and has been the only thing that has stuck, stick with it. Getting into the game of trying to find the "perfect" note app will send you on a path to madness. The perfect app doesn't exist; they are all a collection of trade offs. I once watched an Ali Abdaal video on his note taking system and it was insane. He convinced himself that it was a good idea to have 4 different apps for 4 different kinds of notes, or something to that effect. This is not a place anyone really wants to end up.