http://www.npr.org/blogs/thetwo-way/2013/06/09/190092800/bus...
Given the very limited number of hard, verifiable facts about these programs, whether you believe or disbelieve this explanation is almost a matter of faith.
In the investigation of the Hariri assasination such analysis was employed by painstakingly looking into millions of phone calls in Lebonan. If I remember correctly, the UN investigation team identified 4 rings each color coded (red, blue, yellow, and purple) each ring would only call phones in their ring and the ring leaders talked to each other. So you had nodes that talk to each other and one single node would talk to one other node outside of each group. They also correlated the timing of the calls and locations in relation to where the Hariri convoy was on the day of the assassination (eg. a green call made as Hariri left his palace.)
I can't remember the details but the report was a very interesting read.
http://www.time.com/time/world/article/0,8599,2089420,00.htm...
http://www.cbc.ca/news/world/story/2010/11/19/f-rfa-macdonal...
Potentially it's an effective way to identify folks who might deserve more investigation. Though it's highly questionable how effective it is as a means of stopping crime or terrorist attacks.
This excellent article was on the HN front page a few days ago:
http://kieranhealy.org/blog/archives/2013/06/09/using-metada...
But it probably also includes location, if only the cell tower used.