I am in the process of building a Chrome extension, and for the whole thing to work the way I would like it to, I need an external JavaScript script to be able to detect if
Your extension could interact with the website (e.g. changing variables) and your website could detect this.
But there should be a better way to do this. I wonder how Google is doing it on their extension gallery (already installed applications are marked).
Edit:
The gallery use the chrome.management.get function. Example:
chrome.management.get("mblbciejcodpealifnhfjbdlkedplodp", function(a){console.log(a);});
But you can only access the method from pages with the right permissions.