Assembling my Network, one of the blogs I follow, is running a series of posts about network analysis using the igraph package of R (see Part I of III and Part II of III). I’ve expressed myself elsewhere on how useful R is (the diagram below is just one example), and these posts do a very good job of explaining the network-related aspects of R.
Update 1: see also the sequels: More food web plotting with R and Part III of III. The latter post looks at the Otago Harbour intertidal mudflat food web which I have posted about before. There will surely be more posts about R and food webs to look forward to on this blog.
Update 2: this content is now also on a page at this blog, for more convenient access.