I'm a nonprofit ED with a small organization (less than 5 full time staff). I don't know what area of the country you're in or how your industry experience relates to whatever nonprofit you're interviewing for, but I think something that can help prepare for the interview is determining the questions YOU have for the organization. Jot them down and take them to the interview - at the very least, you'll appear well thought and prepared.
Offhand, my initial thoughts knowing nothing about the job -
1. How big is the staff that I will be tasked with managing? What are their roles/ responsibilities, etc.? Often times small organizations are plagued with "everyone does everything" syndrome and there's less organizational structure. Not a bad thing, per se, but it can present challenges that you'd want to be aware of.
2. What is the annual budget of the organization and the revenue streams? Do most of the operational funds come from inidividual ("bread and butter") donors, or major gifts? How much (if any) foundation/ government/ grant funding does the organization strive to get each year? Is there a development team or staff, or does the ED primarily responsible for fundraising? How active is the board of directors in fundraising? These last two questions are key because my experience has been that they expect the ED to do the heavy lifting of fundraising in small organizations that lack a full development team. Ask to see annual reports from the last several years (this will give you a clue as to how organized the organization is and/or how much work it needs).
3. Ask about the board. Is it a working board, or primarily a governance structure? How involved are they in programs, fundraising, operations, etc.? How often do they meet with the ED and are the ED expectations clearly laid out in a job description and annual reviews? How big is the board? Are there term limits (if not, RUN)?
4. Who was the previous ED? (If the answer is "the founder" - consider your options very seriously.... replacing a founder is not fun or easy)
5. Does the organization have a strategic plan? Is their mission clearly defined? Do they have ways of measuring not just output but IMPACT? IE, there's a difference between tracking how many meals a soup kitchen puts out each year and tracking how many homeless families/ individuals were able to transition into more permanent housing as a result of the organizations programs. Not to sound hyper critical, but lots of small organizations sprout up and work for years on short term rather than long term measures, and with the fundraising dollars harder to come by in a competitive nonprofit world, every organization has to identify its value and sustainable impact much more intelligently.
I'd say talk/ ask about best practices and how the organization ensures that its reviewing recent research on whatever issue they are fighting (poverty, domestic violence, recycling, etc.). Academics in sociology and other fields are very actively adding more and more knowledge about how habits change/ sustainable impact can be best implemented, etc. And you want to make sure the organization you're going into is open to and/or already using the most recent research available.
I hope this is helpful. As I said, not knowing the specifics (which is fine) means I'm throwing giant darts at your situation. I'm sure if they are calling you for an interview you've got a great track record to begin with. Good luck!