I have been trying to use the awesome Orgmode (Emacs) together with DT for a while. One of my biggest issues was that the DT links were not clickable in Orgmode. Adding the lines below to your init file (.emacs) solves this problem.
I thought I should share this.
;; DevonThink Links
(org-add-link-type "x-devonthink-item" 'org-devonthink-item-open)
(defun org-devonthink-item-open (uid)
"Open the given uid, which is a reference to an item in Devonthink"
(shell-command (concat "open \"x-devonthink-item:" uid "\"")))
In fact I am not using GNU Emacs, instead I am using Aquamacs, which is an Emacs for Mac with many nice and extra features.
The nightly builds of Aquamacs, which turn out to be very stable, are based on Emacs 24. The most important thing about Emacs 24 is that it has a package manager ! So you can update packages with no hassle. This way I am able to use the cutting edge versions of all packages, including Orgmode 7.4.
Together with the sync option through Dropbox and MobileOrg, which is freely available for iOS and Android, Orgmode became even more awesome.