strangerland®gmail.com
Eclipse (I haven't figured out how to use this well, but the editor is much more powerful then jEdit for java)
JUNG2 (and the maven repository)
JSoup (and the maven repository)
CentiScaPe 2.1 Plugin for Cytoscape Source code located at https://bitbucket.org/giovanniscardoni/centiscapepublic which computes centrality measures for graphs in Cytoscape
Git
MinGW with gcc-java
Cygwin with svn
Numerical Recipes
Wikipedia
https://books.google.com/books?uid=117642318727646225336&source=gbs_lp_bookshelf_list