There are a couple of different ways to handle this. The first, and simplest, is to look for the "hook" the plugin adds. For example, the barcode plugin adds methods to a cordova.plugins.barcodeScanner object. It would be trivial to see if that exists. Cool, problem solved, right?
Well in his case he was using InAppBrowser. This plugin simply modifies window.open so it isn't something you can really (as far as I can see) introspect. I did some more digging and found something interesting.
If you look at the platform build version of your www code, you will notice it includes a cordova_plugins.js file:
If you open it up, you will see a list of any plugins you have installed. I opened up cordova.js (honestly, I don't look at it often, but I should) and saw that cordova_plugins.js was being loaded in dynamically and parsed. My assumption is that this has to happen before deviceready fires so you can safely use any plugins you've got installed. On a whim then I tried the following code inside my deviceready:
var md = cordova.require("cordova/plugin_list").metadata;
metadata part came from what I saw in cordova_plugins.js. While the rest of the file has random stuff based on the plugins installed, metadata appears to be just a list of your plugins. I confirmed that this worked well:
So - that's it. I should note that I spoke with Shazron and he mentioned that if you used browserify, it might mess with how the JS file is generated. I'd say use with caution and let me know (via the comments) how it works for you.