Now that it's out there I can show you how I did it.
The trick is this -- the bookmarklet calls an app running in a web page on fargo.io.
This is where the app is: http://fargo.io/misc/bookmarklet/.
Here's a screen shot of the source of the app.
Because that app comes from the same domain as the Fargo app, when they're running on your machine they share a local storage namespace.
The app writes the query string to localStorage.fargoSearchString, and it quits.
Once a second, Fargo looks for localStorage.fargoSearchString. When it shows up, it copies it, deletes it, and then parses it, and adds the link to the designated linkblog outline.
We just communicated with a running app without having to relaunch it. Which of course with a major piece of software like Fargo is a fairly big deal -- far too much work to do for a single link. But the intermediate app is just a few lines of text. No big deal loading it just to send a message to Fargo.