Travel agencies (like Orbitz, Expedia, etc) could use any ticket stock of one of the carriers in the itinerary, or an authorized GSA ticket stock. Generally the one used will be the one that has IET agreements with all carriers in the itinerary.
For example, if it was UA, LH, and KC on an itinerary, and UA doesn't have an IET ticketing agreement with KC but LH does, then the system will automatically choose LH as the ticketing carrier. If both UA and LH have agreements with KC, then it's anyones guess which will be chosen, but IATA does have a general guideline:
Standard IATA Rule
First International Carrier, or
First Transatlantic Carrier, or
Predominant Carrier – The carrier that has a majority of TPM (miles) in the ticket
Selection of the Ticketing Carrier as per IATA Reso 852
The Ticketing Airline shall be:
Any BSP Airline participating in the transportation, or
The BSP Airline acting as the GSA for any airline participating in the transportation, or
Any other BSP Airline providing the Agent has received written authorization from that BSP
Airline to issue E-ticket for such transportation
Since this is going to become an issue in 2014 for UA fliers, might want to train yourself on some IATA regs concerning this (specifically resolution 852).