I use priority mail shipping boxes. Most PCBs fit fine. (even with PCB feet on them) They're sturdy enough to stack like a totem pole. They're free. And, if you decide to sell the PCB later it's almost ready to ship.
If you want something that looks better than a stack of usps boxes, Uline sells sturdy pre-cut shipping boxes in a few PCB-ish sizes. Plain brown cardboard boxes with fold-in 'locking' flaps... similar to an MVS kit box. I might transition to those soon and print some fancy labels for the sides of the boxes. You have to buy in quantities of 50+ though.