PCB Panel Size for Maximum Manufacturability
The panels actually used are something like 18" x 24", for your internal panelized PCBs using about letter size (A4) is probably reasonable as a first cut. 

The PCB house is not the only, perhaps not even the main, consideration. You have to make sure your assembly houses can all handle the size of the panelized boards or your assembly costs will skyrocket.  

You should put tooling holes in the tooling strips and fiducials, plus additional fiducials around BGAs and such like.