In order to differentiate between the Incognito and the Regular Chrome window, I wrote this simple extension that adds a postfix to the title of Incognito tabs. This way, it's possible to recognize those windows from scripts (wmctrl, AutoHotkey).
It greatly improves my workflow, yet it's so simple, so I've decided to share it.
I've added in the README an example script I use on my Linux and Windows machines to toggle the browser windows using this extension :)