I have a number of colleagues who have alternate names that they use
along with their full names, some of them use these alternate names
when publishing.

For example:

Ping Zhang and Na (Lina) Li (2005). The intellectual development of
human-computer interaction research: A critical assessment of the MIS
literature (1990–2002). Journal of the Association for Information
Systems (JAIS), 6(11):227–292.

My colleague's family name is Na and her given name is Li, she
prefers the Chinese form of family-name, last-name and thus uses her
full name contracted to Lina as one in the west would one's first
name, while retaining the individual elements for official
documents. Because she is known by this name she wishes to have it
used in publications. I imagine that similar situations abound.

(Say, if Lina ever comes across this email archived somewhere, hi
Lina!, hope you don't mind me using your article as an example ;)

I had a look at the userguide:

http://www.loc.gov/standards/mods/v3/mods-userguide-elements.html

could it be a type of termsOfAddress? Doesn't seem right.

Any ideas? I searched for information in the regular citation style
places but not very hard, so if there is a recommended way of coping
with this I'd be more than happy to be referred to the appropriate
guidelines.

Thanks,
James