http://www-personal.umich.edu/~mejn/netdata/
This page contains links to some network data sets I've compiled over the years. All of these are free for scientific use to the best of my knowledge, meaning that the original authors have already made the data freely available, or that I have consulted the authors and received permission to the post the data here, or that the data are mine. If you make use of any of these data, please cite the original sources.
The data sets are in GML format. For a description of GML see here. GML can be read by many network analysis packages, including Gephi and Cytoscape. I've written a simple parser in C that will read the files into a data structure. It's available here. There are many features of GML not supported by this parser, but it will read the files in this repository just fine. There is a Python parser for GML available as part of the NetworkX package here and another in the igraph package, which can be used from C, Python, or R. If you know of or develop other software (Java, C++, Perl, R, Matlab, etc.) that reads GML, let me know.
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