The Sweet Setup has Shawn Blanc’s Detailed Ulysses Setup, which is compelling in its comprehensiveness. He appears to have all, or at least much, of his writing life/work operating in and through Ulysses:
I think much the same could be done in Devonthink, though I am not sure about the custom folder icons, which really do, I think, make a difference in terms of UI and UX.
The idea of an internal content management system (CMS) is of course very appealing. For a long time, I ran much of my thinking through previous iterations of this WordPress blog. Then I got burned by a couple of incidents, and, too, I fell in love with having everything in plain texts (and not necessarily XML). But having developed a reasonably good journaling habit using Day One, I feel a little less compelled to insist that everything has to be in an open format. As long as you can get it there with a relatively small number of steps, I am willing to give it a shot.