Here's a good, open-ended question to ask: "What do you find is the best thing about working here, and what's the biggest challenge?"
This question is another one designed to get the interviewer talking. You're showing that you value the interviewer's insight and opinion. You are showing that you understand that even the best organizations will have their problems, and you are suggesting that you aren't afraid of a challenge. If the interviewer responds candidly, you also might learn a lot of information that you won't necessarily find on the organization's Web site or in its annual report.
Read on for some questions that get to the heart of what you care about.