That's what I use, but it's still just a list of text notes with little or no formatting. I think hyperlinks exist but that's it, unless I'm missing the other features.
This fork of Notational Velocity adds a third pane which shows formatting using markdown.
If you are willing to learn markdown, and it's pretty darn easy, you can add formatting while maintaining raw text format.
I like markdown enough though that I find I write in markdown, and just hide the preview pane that includes formatting. I just don't really need it.