It IS a bit like running around in circles chasing one's tail. I've kind of settled into a cocktail of DOpus, X1, Locate, Evernote, TNP, and Net Snippets.
I'm in the same boat. I use multiple notetaking softwares simultaneously. I use Evernote anytime I want to save information, but I'm not sure if I really need it or not. I don't even attempt to organize it, I just dump it all in Evernote. Also, for any web capturing I'll also use Evernote.
For more important notes that I need better organization for, I use myBase, although I think I am going to switch to Texnotes Pro pretty soon.
Surfulater, to me, is still the best if a large portion of your notes come from the web. Unlike Evernote, it offers advanced organization features like most hierarchical programs. I do very little web capturing, that's why I just dump them into Evernote.
I also use DOpus and Locate, but I don't consider that part of my notetaking process. That's just file management to me. I used X1 for a while, but I really don't have a need to search deep within the contents of my files or emails or whatever.
Maybe you are right, Darwin. Perhaps it's better that there isn't one application that does all aspects of this entire process well. I've never liked all-in-one apps because they just don't work as well as specialized products. Maybe the Frankenote that I talked about in my review isn't such a good idea. I just had an idea; in the followup to my notetaking roundup, instead of delving deeper into the features of the programs again, maybe I'll talk more about the philosophy of the programs, and relate them to what program is suited for what user.