Graphs with labeled edges seem clearly better. But then what if you want a relationship with more than two members? (Or less! "Not" and "maybe" are two important unary relationships.)
Once you've reified your relationships that way, you'd like to be able to search intelligently through them. "Ordinary" knowledge graphs let you see all of a thing's children, or parents, or maybe in some cases all it's descendents and ancestors up to some level of recursion. Better would be something that lets you ask targeted questions, like "Show me everything Sally has asked me to do that does not require a computer."
To my knowledge there's only one program that lets you reify your data and query it in the ways I've described. It's called Hode, for Higher Order Data Editor. I wrote it.
How much work does it take you to add your notes to it? I'm curious about it on two dimensions:
* The time it takes to add a note
* What decisions you need to make to add a note (what to link it to, what not to)
You've zeroed in on the weakest point of the program. Adding notes is mechanically easy but conceptually hard. That's because there are many ways you could choose to represent the same concept.
For instance, suppose "harry gave sally a book" is in your graph. One way you could represent that is "Harry #gave Sally #object a book". Another is "Harry #did (give #object a book) #to Sally". Another is "Harry #did (give #object a book #to Sally)". And actually maybe you'd prefer to represent "a book" as "#a book", so that you can just search for "book".
They're all plausible representations, and all have different implications for how you would run searches. You've got to be consistent in how you represent those relationships, and the program can't help you because I mean it's a database, not a general artificial intelligence.
The strength of the program is that the structure of your index is entirely up to you. But soon that freedom gives way to being bound by the decisions of your former self. And your future self will inevitably understand the space you're representing better than your former self did when it bound you.
Just a thought: if I were interested in adopting a tool like that, my chances of successfully sticking with it would go up 100x if there was a set of "default recommended practices" to follow when saving a new note, to cut down on the decision I would need to make.
Then over time, as I got more familiar with the tool, I could always tweak those default recommendations to fit into my own style
And who better to offer those default practices than the tool's creator? :)