My DD started Prep this year and we didn't ask too many questions - we did a lot of behind the scenes research, talking to parents etc. Questions I asked the school included:

What's the policy on bullying
Do you have a reading recovery program?
What specialist teachers are avail to the kids and how/when do they access them (ie art, library, PE. One school I looked at only had an art teacher and the library was only open 3 days a week).
Is there a no nuts policy?
Is the school a Healthy Eating School (this is a specific program in Vic and restricts what the Canteen can sell) and what's for sale to the kids in the canteen?
Do you have a school nurse?
Do you have a First Aid room?
Do you have before/after school program? (essential for our family)
How many children in each class?

We also observed DD's interaction with the Principal, the teachers, the grounds. One school we went to she told the Principal she hated the school. Another we had to drag her out of! We also watched the kids in the classrooms we visited. We didn't attend a formal open day but made an appointment for a private tour. This meant we got to see teachers and kids in a more "natural" state as opposed to "have to be on our best behavior today" state. The kids were all really happy. I have to say that I've never seen an unhappy kid at our school. And they are all very friendly children.

Good luck - it's a hard decision to make!