There are actually quite a few applications for visualizing and analyzing graphs. [Gephi][1] and [Cytoscape][2] are two well-known open source applications that support large and complex graphs. If you're mainly interested in visualizing graphs, have a look at [Graphviz][3], which is an absolute classic.


  [1]: http://gephi.org/
  [2]: http://cytoscape.org/
  [3]: http://graphviz.org/