Does desktop application include WebGL applications in the web browser?
If so, then you might want to check out skarf.js, a framework that I have written for handling JavaScript augmented reality libraries in Three.js. It currently integrates JSARToolKit and js-aruco, so you can easily switch between these two libraries to decide on the more suitable one to use.
This framework takes care of a number of things for you, including automatic loading of models when the associated markers are detected (association is specified in a JSON file). There is also a GUI marker system which allows users to control settings using AR markers.
Integration with Three.js is just one line of code to create a Skarf instance and another line of code to update.
There are videos, live demos, source codes, examples and documentation available. Check out http://cg.skeelogy.com/skarfjs/ for more info.