From what we know about Citrix, you won’t have any trouble installing and registering Balsamiq Mockups 3 for Desktop on it or on any other virtual environment. You may even find this FAQ on silent installation helpful.
Please keep in mind that you will need to purchase a Balsamiq Mockups 3 for Desktop volume license for the total number of users who will be accessing our app within your Citrix environment. Our licensing is by assigned users, rather than concurrent users. It will be your company’s responsibility to make sure you are in compliance with our EULA, and that only the users you have assigned have access to use our software.
Here is a little more information on our volume pricing and how to purchase it.