I’ve so far seen this exact problem in 4 different apps; Obsidian, Trillium, SilverBullet, and TiddlyWiki.
All of these let you write in some sort of lightweight markup (markdown for most, but TiddlyWiki has its own markup language). All of these also let you add frontmatter or metadata to your notes, and have barrels and barrels of features for querying, parsing, cataloging, and tabulating this frontmatter.
However, markdown is itself structured data. It has headings and tables and lists. That’s structure. Why not have similar facilities for querying the markdown itself?
I got into this on the TiddlyWiki forums. A lot of users encouraged me to put everything into metadata fields, practically leaving nothing in the body of notes. Then why have bodies? Why not just have a vault full of YAML files?
Why can’t I, for example, get a list of all notes where a certain heading exists, or extract data from a table in a note, or count the number of words in a note, or in a section of a note?
I recently learned about Obsidian from a friend, but haven’t started using it yet, so perhaps I can offer a perspective that differs from current users of Obsidian or any of the other apps you listed.
To start, I currently keep a hodge-podge of personal notes, some digitally and some in handwriting, covering different topics, using different formats, and there’s not really much that is common between any of these, except that I am the author. For example, I keep a financial diary, where I intermittently document the thinking behind certain medium/long-term financial decisions, which are retained only as PDFs. I also keep README.md files for each of the code repos that I have for electronics and Kubernetes-related projects. Some of my legacy notes are in plain-text .txt file format, where I’m free-form record what I’ve working on, relevant links, and lists of items outstanding or that are TODOs. And then there is the handwritten TODO and receivables list that I keep on my fridge.
Amongst all of this chaos, what I would really like to have the most is the ability to organize each “entry” in each of their respective domains, and then cross-reference them. That is, I’m not looking to perform processing on this data, but I need to organize this data so that it is more easily referenced. For example, if I outline a plan to buy myself a new server to last 10 years, then that’s a financial diary entry, but it would also manifest itself with TODO list items like “search for cheap DDR5 DIMMs” (heaven help me) and “find 10 GbE NIC in pile”. It may also spawn an entry in my infrastructure-as-code repo for my network, because I track my home network router and switch configurations in Git and will need to add new addresses for this server. What I really need is to be able to refer to each of these separate documents, not unlike how DOIs uniquely identify research papers in academic journals.
It is precisely because my notes are near-totally unstructured and disparate that I want a powerful organization system to help sort it, even if it cannot process or ingest those notes. I look at Obsidian – based on what little I know of it – like a “super filing cabinet” – or maybe even a “card catalog” but that might be too old of a concept lol – or like a librarian. After all, one asks the librarian for help finding some sort of book or novel. One does not ask the librarian to rehash or summarize or extract quotes from those books; that’s on me.
Check out Amplenote. Great for sorting loose thoughts into notes, then into tasks, then schedule them if you want.