Your response will depend on the position and the sector, but in all cases, when they ask you if you have any questions, you should definitely have some ready. The interviewer wants to see if you have done your homework about the organization and are committed to them specifically, so feel free to ask questions about current projects, products, or services that you read about in your research. For an academic job, make sure you ask questions about the department: how it interacts with others, or how interdisciplinary research is supported and fostered, for example.