Barcodes Everywhere
Each and every piece of components is tracked by sticking a barcode to it. Smallest-size parts are not tracked individually, but off the coil they are taken from.
The first step of efficient quality control is a working component tracking system that can identify each and every part from the moment it arrives until it gets used on a particular product (where it can still be tracked using the product's new barcode) up to the PC or notebook. If this is done right, you can scan the product barcode and serial number to track all individual components, batches and suppliers. To do this properly it is important to establish proper incoming and outgoing quality control procedures.
Automated Testing
In the process of motherboard production, several inspection steps are added. There are visual inspections (using the human eye or automated) and ways of doing automated testing using simple electrical circuits for basic checking, or ATE hardware (automated test equipment) to simulare components.
Board testing devices take care of electrical checking.
Automated test equipment will simulate components.
So far there is no substitute for real-life product testing, which is why motherboards are always tested using a real Windows scenario and certain applications or benchmarks.