When contacting universities, in many cases, I find the replies to my emails extremely well detailed and helpful, therefore in such cases I find a simple "Thank you" to be just insufficient.
For example, when you have already applied to a program, and then you email the department to ask a simple question about supplementary documents, but they put SO MUCH effort in their response and even analyze your application before the application process has even started and they tell you that they are very certain that you will be accepted. How would you react? Is it rude to say something like: "I'm very glad to hear that."
In such situations, I do not really know how to best answer the person to show them that I really appreciate their email very much.