A growing number of faculty are using clicker questions and peer instruction in introductory physics courses at institutions across the US; however, this approach is rarely used in upper-division physics courses. At the University of Colorado at Boulder (CU), faculty have been incorporating clicker questions in upper-division courses since 2004 – clickers have now been used 24 times in 10 different upper-division courses by 14 different faculty. We surveyed students in 16 of these classes (including 2 classes of a graduate course), soliciting their perspectives on and recommendations for using clickers in upper-division courses. We find that 77% of the students recommend using clickers at this level. In all classes, a majority of students favor clickers and there are few negative responses. Through analysis of students' responses, we identify what they value about the use of clickers and the perceived mechanisms by which clickers support their learning. Finally, we find broad student agreement on how to best implement clickers in these courses.