I keep trying to use Roam and Obsidian (rather than a more simple note taking app like Notable,) but I find that my more complex thoughts on topics, i.e the ones I would want to use this kind of software to record, is more often than not about external content such as PDFs or webpages. I know you can simply link files or urls inside markdown, but the integration seems a bit simplistic. I suppose some people will just copy and paste highlights, or extract notations, but something like Zotero seems hard to beat for my usage.