The Raspberry Pi is a great example of how automated manufacturing is leveling the playground in the PCB manufacturing industry. The video explains a bit of the process..
The main difference from hand soldering parts is that the automated process uses solder paste instead of solder wire. The solder paste can be applied in a few ways as explained in the next video.
Reflow soldering is the main process used in automated PCB manufacturing. It’s a very simple 3 step process : Apply solder paste , place surface mounted components on the board and reflow with a reflow oven.
Making your own reflow oven is also a fun little project: http://danstrother.com/2011/01/15/reflow-oven-controller/
More reflow options:
Through hole soldering can also be automated by using wave soldering as in the next video.
The last process to cover is the pick and place machine. It picks up components and places them at the pre-programmed spot.