I copied this from the "Your Top 3 Tools?" thread, because I thought it warrants a separate conversation. I am also at a similar impasse:

Vincek wrote:

1. Evernote -- for long term storage of just about everything, including
research/background for blogging and forthcoming book
2. GREAT BIG HOLE (explained below) in workflow
3. Scrivener for Windows -- for (less than optimal) organizing and (very
good) writing capabilities

I envision that #2 could be filled by something like Devon-Think (IF I
used Mac, but I don't), or Connected-Text (if I wanted another
stand-alone program, but I don't). So I wait.... until this hole gets
filled by something that integrates (not just interfaces) with Evernote.
Another way of describing #2 is that I have a boatload of information
that for now I have to make sense of mostly through my own head, but
would be great to have a digital program to augment this process (ala
writing process described by Steven Berlin Johnson who uses Devon Think
for Mac).

I found a link to the following TheBrain forum thread at the TreeSheets Google Group; I especially like the part about the 'information thermodynamics': "There is a conservation between the energy (time, effort) of information entry and corresponding information retrieval." (I believe Steve Zeoli has mentioned something similar in the past).
http://forums.thebrain.com/post/Brain-and-Evernote-Im-in-trouble-6134484

I've written elsewhere that I find Evernote's hierarchical tag features almost as powerful for organising items as any folder-based system. I still do; however, organisation alone is one or more steps before synthesis which is what I often need; it is also not conducive to action.

Hmm, mumble, bumble... (circling in the room a la Scrooge McDuck)