How can I run two instances (or equivalent) of Slic3r on OS X?
You could duplicate the application by clicking on the application and pressing Command (⌘) + D, and then run both - although I'm not sure if that would mess with the preferences. I haven't fully tested it, but both instances opened up and worked, seemingly ok.



You could even rename them to something other than "Slic3r" and "Slic3r copy" to remind you which application is slicing which model, for example:


"TestCube" and "Benchy", or;
"Slic3r-TestCube" and "Slic3r-Benchy", or whatever. 


However, Mark's answer seems much more elegant.