What I have seen, usually companies use two methods for testing boards where you can run software:
1) testing where you place the board on spacers, you connect all connectors and run test software on the board
2) testing when bed of nails was used and you run test software
The first method doesn't need many special additional testing equipment (perspex or wooden board with simple breakout boards). However, this can not be used for huge quantities, because the process of connecting and disconnecting cables is sometimes slow and after some time it breaks and has to be replaced.
The second method was used for thousands of boards manufactured every month, however, the test equipment itself was expensive to create (it was a big box) and basically, to create the test equipment was a project itself. Google for "bed of nail test" and click on pictures, you will see the boxes, but could not find the one we were using (here I found some examples - I have never used this company and I do not know it, it is just for ilustration:
http://www.test-x.com/ )