Other apps I have tried and used over the years:
- http://www.mweb.im/ (markdown) - https://ulyssesapp.com/ (markdown) - http://lightpaper.42squares.in/ (markdown) - http://alternoteapp.com/ (Evernote GUI) - Many, many others
Notebooks really stands out because it has a great iOS app, syncs via Dropbox (plain files), and handles TXT/MD/HTML + Custom CSS&JS.
The Mac app is not great, but it's adequate. I frequently talk to the author and they are rewriting it to be more "Mac friendly", but that's a bit away (1 year maybe?).
For the longest time, I tried to stay true to Markdown, but as I get older, I just want things to be easier, and to look nicer, and I now prefer writing everything in WYSIWYG. Since I have custom styles, I can stick to standard structure (ie H1, p, ul, ..), which is in spirit close to Markdown (ie structure only). And I can still customize when I want complicated things (I wrote a couple special classes for some use cases).
Plus, it works with the filesystem, so you get folders, which I personally prefer to all this tagging BS. It makes it easier to have everything in one place: work stuff and personal stuff, and to keep it all neat and tidy. Also, because it's files, it's always available offline (iOS app too).
The iOS app is like a small file manager, so I also keep pictures, PDFs, and some other docs. So I always have all my important stuff on hand, no matter where I am.
Overall, I think it's a great app, which still has room to grow (better GUI on desktop, encryption, ...)