What does "run a panel" mean in the context of PCB/PCBA fabrication?
Like Olin said.  

Making a layout of the PCBs on a panel is called a panelization. In most cases V-cuts will be made between PCBs, so they can easily be separated by bending the panel. Care must be taken with high components (e.g. connectors) close to the edges, that they don't prevent the bending.
Alternatively a panel may be milled so that the PCBs are only connected at a few points. These connections are perforated so that they are also easily separateble. Milling is more expensive but may be required for the PCB; they are more precise than V-cuts, and also if your boards isn't rectangular you'll have to mill the edges.

A panel will at least have a couple of edges on opposite sides where the PCB manufacturer will place fiducials.  



These are small marks, as copper circles, which are used by the pick-and-place machine as reference points to know where the parts should be placed. Here there are just 4 fiducials on the edges, but I've seen them as two rows at the top and bottom of the panel.

Panels will often have a number of identical PCBs, but you can make a panelization of different PCBs: