Way back when, we were trained to hold our questions until the end of a job interview. This is no longer good advice. Instead, I encourage job candidates to ask questions as they come up in the interview. To ask relevant, thoughtful questions, do some research about the company and the position before hand.
For example, when asked what makes you qualified for the position, you would respond by stating your top three qualifications, having examples, and then asking whether those skills are the type they are looking for in this position.
Another example might be to ask who the position supports or how it helps the company achieve its goals. Other questions might include “What type of software do you use to help your company run efficiently?” or “What do you view as being the most important aspects of the position?”