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I tend to keep the majority of my Notes and References outside of OmniFocus.

Currently I have the following setup:

. Evernote to capture all my references, clippings, and random captures of my everyday. I also sometimes use AwesomeNote on iPhone since it offers a nicer User Experience for Note Taking and directly connects with Evernote

. Notebooks on iPhone and iPad to take robust notes (I can then send any notes directly to OmniFocus if I decide that the note should be associated with a task. I can either include a link if I am still working on the note, or Send the text of the note directly to OF)

. On the desktop side of things, I use Notational Velocity to connect to my iDisk where I store my Noteboooks notes (it allows me to edit my Notebooks notes from the desktop)

Now, my ultimate dream is to have a totally agnostic Notes system so I can take notes and then be able to link 1 Note to N# of Tasks and have all three versions of OmniFocus connect to it.

My current frustration is that I could take all my notes in Evernote, but the iOS versions have no way of connecting to the link I create in the Desktop version. In addition to this, the Notebooks app is only good for the iOS device, and the linking to a note only works in iOS.

I really wish Notebooks was on the desktop, or that OmniFocus played nicer with Evernote (the way Nozbe does).