Susan that will depend on what the flagstone is being set on and how big the spaces are between them.
Fine gravel works well if the spaces are fairly large, Some people simply plant grass there as well.
For tighter spaces there is sand mix that has a cement product incorporated with it made just for that use. It hardens once it becomes wet. Its is spread down pushed in with a broom then wet with a hose to harden it. This type of project works well with paving stones and bases that are fairly firm as it can crack easy if the ground below moves with the flag stones.
What are you placing the flagstone on?
They will be on a bed of sand that is placed on top of crushed stone. I knew there were different fillers but wasn't sure what the advantages and disadvantages were. I think the fine gravel would still allow weeds to come through, the sand-cement mix product sounds better.
@Susan it is called polymeric sand in CANADA.... works great.. keeps ANTS our too while sealing the seams of the pavers... Love it.. does not wash out!!!
Crushed Granite is what I like to use, stay's in place nicely.