Just a quick video showing how I depanelize PCBs. I typically buy PCBs from SeeedStudio or iTeadStudio and it makes sense to use the 10cm by 10cm board size and jam more than one PCB into that area. Diptrace (my schematic/PCB weapon of choice) makes it easy to panelize multiple designs, but its relatively easy in Eagle as well as others.
The CNC machine makes it easy to separate the boards out when I get them back. The same could be done with a bandsaw if that is what you have at hand. Basically I dump a DXF out from the PCB with the board outline and the 2mm silkscreen lines that I draw on the PCB to separate the various boards. Depending on whether I want something more fancy, I either bring that into QCAD (fantastic 2D drawing tool) to add goodies or straight into CamBam (amazing CAM tool for CNC).
I first get CamBam to make a pocket for the PCB so that I can align the PCBs the same for all 10 boards. I then create an engraving path along all the board separation lines. I’m a chicken so I always do two cuts, 35mil deep each. I use a 2mm 3-flute endmill and 12 inches per minute as a feedrate when cutting PCBs. My spindle speed is somewhere around 3200RPM if I recall correctly.
I use carpet tape to hold the PCBs in place in the pocket I cut and its off to the races. A shop-vac takes care of the dust.
I spent the weekend bringing one of those boards up… a 32 channel servo controller. More on that to come.