The widespread use of the surname "Nguyen" traces back to many centuries ago. The earliest example of the surname becoming widespread goes back to the early 1200s when Trần Thủ Độ overthrew the Lý dynasty and established the Trần dynasty through a number of controversial methods (most famously involving a forced marriage). In the process, he forced a number of the members of the Lý dynasty to change their surnames to "Nguyen."
There were similar power upheavals over the next few centuries where descendants of various dynasties changed their surnames to Nguyen (in an attempt to avoid retribution) following the collapse of various empires (the Hồ dynasty and the Mạc dynasty for example).
In the 1800s, the Nguyen dynasty seized power, leading to another wave of changing surnames (due to force, fearing persecution, etc.). It was also not uncommon for people in Vietnam to take their names from previous Emperor's names, and the Nguyen dynasty was the last dynasty of Vietnamese emperors. The dynasty ruled over the period of 1802-1945.
In summary, the surname has made its way through centuries of Vietnamese history due to power struggles, dynasty changes, and the changing of surnames to avoid persecution as well as simply for extra privileges and advantages in terms of things like jobs and power (and even to show loyalty). Today, [~40% of Vietnamese people have the last name Nguyen] (http://www.theworldgeography.com/2012/02/10-of-most-common-surnames-in-world.html) and because of the way the surname has been passed down, by itself it doesn't really give an idea of a person's social/regional standing or whether they are related to another Nguyen (unlike in various other countries).
For more information on this and/or Southeast Asia in general, [this encyclopedia] (http://www.amazon.com/Southeast-Asia-Historical-Encyclopedia-Angkor/dp/1576077705) is a fantastic resource.