There is already too much note-taking software out there, but it's not what I expected. Some programs use the file system and markdown, which is great, but not enough to manage attachments.
Discussion
It and a CMS are two things, but they both manage similar content. The intersection between them is probably the wiki. Theoretically, notes can be automatically published on a given site with a simple addition of some metadata, but few note-taking software do this.
Markdown has a number of plugins that can render content from source text. Notes should be able to include more formats, such as sheet music. There are also more features that could be integrated within the software, such as GTD and so on.
Whether from the file system or the markdown structure or the block hierarchy, the base structure of notes should be nested lists. Everything should be a list, and the depth of markdown headers should be ignored. The top level header of the exported content is the h1.
Notes are books. Reading and writing notes are very close to each other. Software should make it easy to bring in, and read, the public notes of others. A wiki is nothing more than a group of people's notes. Imagine a map of personal notes linked to the knowledge of the world.