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MatlabBGL
A Matlab package combining Matlab sparse matrices and the Boost Graph Library for high efficiency graph algorithms.
vismatrix
A interactive generalization of Matlab's "SPY" command written for OpenGL is one tool for researchers to examine and explore sparse matrix structure.
libbvg and bvgraph
Sebastiano Vigna and Paolo Boldi wrote a nice set of papers and code for compressing graph structures. libbvg and bvgraph are C and Matlab implementations of their routines
gaimc
Use graph algorithms in pure Matlab code that aren't terrible slow.
Old
My older software page has a number of small projects that aren't listed here.