Lara Croft: Tomb Raider features several characters visiting Angkor Thom during their trip to Cambodia to recover the first piece of the Triangle of Light.
In The Judas Strain (A novel by James Rollins): The characters are on a journey to find a cure for a plague, and are following in the steps of Marco Polo.
In The Golden Pagans (A novel by Peter Bourne c.1956): The main characters are sent to Arabia during the crusades, captured and forced into servitude by the Khmers. They build a portion of what becomes known as Angkor Thom.
In Patlabor the Movie 2, the opening scene appears to be based on the Angkor Thom, as said by Hayao Miyazaki in an interview with Animage magazine on October 1993.
In Civilization IV: Beyond the Sword, Angkor Thom is the third city to build in Khmer Empire after Yasodharapura and Hariharalaya.
In Eternal Darkness: Sanity's Requiem, Angkor Thom is the region where a Cambodian temple is located, housing the Ancient Mantorok
