See a the poll here by Gabriel Rossman at Code and Culture. I voted for R and ‘igraph’. If you use R you are getting access to all the other wonderful things that come with R. Using specialized package, like Pajek, UCINET etc requires constant going back and forth between network software and some other 
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).
