Software were the instructions designed for computers to perform specific functions.
The Doctor's sonic screwdrivers all used the same software despite various different models, effectively mirroring the Doctor themselves - "same software, different face." The Doctors used this to their advantage to make centuries-long calculations in seconds (given the process was started by the War Doctor's sonic screwdriver as a subroutine that worked right up during the Tenth Doctor's time and completed four hundred years later by the Eleventh Doctor's time) in an attempt to break down their cell door molecularly while imprisoned in the Tower of London. (TV: The Day of the Doctor)
Jeff Atkins worked in software in 1999. (PROSE: Bide-a-Wee)
I2 was an Earth software company created by the Voracians. They planned to use the living software program Voractyll to take over the Earth, but were stopped by the Fourth Doctor. (PROSE: System Shock)
Yukio Nakaguchi and Sulio N'Farr maintained the software for Project Eden. (PROSE: Lucifer Rising)
Owen Stanford was a software designer. He and his team won the Chesterton Award in 2010 at a conference for their work. (AUDIO: Situation Vacant)
Code Nine was a priority alarm initiated when computer software — activated on the release of the Emergency Protocols — detected important words. (TV: Aliens of London)
Calling the Doctor - Doctor Who - BBC
Calling the Doctor through the Sub-Wave (TV: The Stolen Earth)
The Sub-Wave Network was a piece of sentient software programmed to find anyone who could help to contact the Tenth Doctor. (TV: The Stolen Earth)
Dorium Maldovar was given a bag of sentient money by the headless monks in return for security software. (WC: Prequel (A Good Man Goes to War))
After escaping the laboratory where it had been built, the Hadax Ura went to the planet Unnamed BX-4. It uninstalled all of its diagnostic software, becoming insane as a result. (COMIC: Spirits of the Jungle)
Rex Matheson ran some footage through Central Intelligence Agency software to translate it from Mandarin to English. (TV: The Gathering)
Neuroware was software that was implanted into a person's skull. It allowed a person to access the datanet. (PROSE: Second Chances)