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 general analytical software (SAS, SPSS, what have you).
I also use both R packages. Mainly ‘igraph’ (and that is what I voted for) because I find the network data manipulation much easier than in ‘network’. I believe it is also much more efficient computationally than ‘network’ (Gabor Csardi showed couple of comparisons on UseR 2009). On the other hand with ‘network’ you get access to ERGM and all the other statnet packages written by people at Stats Dept at University of Washington. So igraph/network is not an easy choice.
I’m actually working on reliable routines that will convert igraph objects to network and vice versa. Perhaps an ideal situation would be to have a an umbrella interface to igraph, network, graph etc. very similar to DBI as an umbrella over RMySQL, RSQLite etc…..