[prashnts]

I've been using iOS and Mac's native notes app to do that. In my opinion what these solutions lack is an integration between both note-taking (I sometimes like to write a few sentences relevant to a document, and I'd like to have it shown right next to it) while also letting you have the individual documents available in PDF or whatever if you need. Notes app does it perfectly now after iOS 11.1 and High Sierra.

An example is this screenshot from my notes https://imgur.com/a/xuZqW

[lucaspiller]

As long as you don't mind being tied into the Apple ecosystem (and trust they won't loose your data) it's a good solution. Notes used to be backed by IMAP, but the new 'rich notes' since iOS 9/OS 10.11 is backed by iCloud.

[mark_l_watson]

I used to use Notes but stopped after trying to back up my notes. For me, exporting one note at a time to pdf is not good enough, and finding the opaque binary file in ~/Library does not help because it is not a standard file format.

I switched to using Notes in Fastmail.

[davidrupp]

I've been using http://writeapp.net/notesexporter/ for Mac's Notes app; happy with it so far.

[zhoubear]

Right now you can enter comments for a document that's already uploaded. A few UI tweaks could be added to show the latest comment under the document preview.

Exporting to PDF sounds like a really good idea.