The prisoner number of Sonny Troyer 16309 is the same as the prefix code of the USS Reliant's shields to be lowered in Star Trek II The Wrath Of Khan. The writer may well be a fan. Later in the episode Claire Williams reveals her flat number to be 1701 Pike's Way. 1701 being the Enterprise's number and Pike being her first TV Captain.
At about 30 minutes into the episode, it is said that the woman on the roof is in the line of work of "Statistical analysis and data reconfiguration". This is coincidentally what Chandler Bing does on the TV show, Friends. It may be a coincidence, but Detective Lee Scanlon follows with "whatever the hell that is." Which could possible be a nod to the fact that no one ever really knows what Chandler does. The writer could be a fan, possibly written on Friends, or both shows were aired on NBC and are keeping this joke in the network family.
Sonny Troyer played by Eric Stoltz refers to forensic science and CSI. Patricia Arquette played the lead character Avery Ryan on CSI: Cyber.