Pyramid Deliveries was a freighting company.
Pyramid Deliveries trucks could be seen driving around Manhattan. One even drove by Edward Blake's apartment. A freighter is occasionally stops near the Institute for Extraspatial Studies to refuel, annoying Bernie who sits there blocking access to the power hydrant, and the driver talks with Bernard.
Unidentified persons hired freight handlers for illegal things but they ended up dead in alleged accidents. A freight driver (the one seen with Bernard) was given by his boss, the freight co-ordinator, two anonymous envelopes, one with money, one with orders, to deliver to a reliable hit contract. The boss then fell under a subway train. Roy Victor Chess was given those envelopes, and made the assassination attempt against Adrian Veidt.
PD was also behind the creation of the alien, as a Pyramid Deliveries ship carried the designers of the alien from the island they worked on and exploded, killing everyone onboard, including Max Shea and Hira Manish.
Nite Owl II and Rorschach discover that Pyramid Deliveries was headed by Veidt, and that he was behind Dimensional Development, the plot against Dr. Manhattan, all the deaths, even his own assassination attempt.