This seems to be something that pops up on Hacker News quite regularly. My note taking was already very similar, but without tags (which I've now added).
The most important thing is that the system does not get in the way. That's one of the reasons this website is completely written in raw html. I'd get too bogged down in frameworks, getting things running, etc. It would get in the way of actually having a website with content.
It's a lesson that can be applied in many areas; don't get bogged down in details at the expense of actually achieving the end goal.
Notes should be atomic and should contain knowledge instead of information.