nice! So, you are going more for the "mind map" approach right? I am a bit confused now. So links, notes, blog posts, and other 'items' you named on your first answer would be nodes here? I see how it would be very easy to find the category you are looking for, but how would that visualization help at the time to find a specific node? When you said "blog posts", "articles", "projects" where you mostly meaning a way to link to them, or to embed them into the app itself? In other words, is this a bookmarking tool or also a publishing/blog tool?
My idea is quite in a different direction. My best solution so far is http://multikanban.com . It really is just a personally customized kanban board. But it lets me navigate through multiple boards, each board is a project/goal/collection of tasks (maybe like your 'categories'?). Inside each board I store several things, notes, bookmarks, etc. And due to it being a kanban it helps me in the progress of getting it done too. Getting it done might mean several things, for example I have a Kanban board for books I want to read, so getting something done there means I just read a book. It serves both the purpose to see what I want to do, and what I've done, ad it helps me prioritise it too. However, it has lots of limitations.
Even though I'm quite happy with that solution, I want to complement it with something more along the lines of blog/publishing. I do have a blog, but I barely write there. I want to find something in between the small notes and the long blog posts. Which serves the purpose of storing thoughts, links, and categorizing it with tags, but without each entry needing to be a post, as we are used to in common blogs. I'm still conceiving it...if that wasn't obvious yet haha