I've used Circus Ponies Notebook for years, and still do. I may just continue until it stops working!
I just recently tried both Notebooks and Together. Both of which just seem not much more than a specialized Finder app, especially Notebooks. They just aren't the organizational tool Notebook was. I also like(d) Microsoft OneNote when I was a Windows user, but found the Mac version dreadful.
Edited February 2018: CPN no longer works in High Sierra. I ended up using Growly Notes as a substitute. Although it does look more like One Note than CPN. For notes to accompany my writing I can to the realization that the ability of Scrivener to hold every type of reference material and keep everything with the document being written was a big plus I should have been doing all along.