Then I found evernote-mode for emacs and thought I had found the solution. I hadn't. I could see that is was useful, but it didn't really fit with how I work, even though I spend a lot of time in emacs. I realised what I wanted was something like the amazing todo.txt but with Evernote as the backend. Then I found Geeknote and I could tell from the tag line "Are you a geek? Do you like Evernote? Geeknote - is for you!" that I had found what I wanted. I got it installed without too much trouble, and logged in, which I was pleased to see supported the two-step authentication that lets me sleep at nights. I just needed to change the editor to emacs (actually 'emacsclient -t', but that is for another post, maybe) and I was set. I could create new notes, complete with my Secret Weapon GTD tags, edit existing notes, re-tag notes to change priorities, everything I wanted. I love the search functionality and the ability to refer to notes from previous searches simply by their number. I now have set up a bunch of bash aliases to add new tasks and view what I should be doing. It isn't quite there yet but I will tweak and expand on my workflow.
For those that are interested this is in my .bashrc at the moment:
These just allow me to quickly add notes with a priority then view notes by priority. I just need to type show.todo.now and I know what I should be doing. I will probably add more wrapping to simplify some tasks such as changing the priority of a task etc, but for now I am just loving the way I can add a note at the command line and within seconds it appears on my phone's Evernote widget, amazing integration. Also in reverse I can add a reminder on my phone while dropping the kids at school and find it waiting on my command line at work ( after typing todo).
I will try and post more of my config and experience after I have used it for a while and see how it fits with my workflow.