I would say if you have a mixed audience and don't need the extra features that AFCS for Player 10 offers, just build for Player 9.
Player 10 can run Player 9 SWfs just fine.
If you need the extra features of AFCS Player 10 (rtmfp, p2p support, etc.) you'll need to build two versions of the applications.
They will still be able to talk to each other (i.e. it's ok to have some users with Player 9 and some users with Player 10) but you may get into cases where users with Player 10 will be "downgraded" to Player 9 functionalities (i.e. they will not be able to use p2p)
If you really have a case where you get an error when users connect in a mixed environment please send the details and we'll look into it.