Software
http://processing.org/ - this needs a gridbag
someday, when I get time (like all the other someday items) - http://www-128.ibm.com/developerworks/java/library/j-mylar1/?ca=dgr-jw17Mylar-1
Advanced modelling
http://www.visual-literacy.org/periodic_table/periodic_table.html - periodic table of visualization methods
http://www.maintainj.com/ - eclipse - create sequence and class diagrams from running code - they're in Toronto ! Is it OSS though?
http://www.se.eecs.uni-kassel.de/~fujabawiki/index.php/EDOBS#About - OSS - eDOBS is the eclipse plugin version of the Dynamic Object Browsing System. It visualizes object worlds and thus makes it easier to imagin what happens when certain actions are done. So you can actually _see_ what happens when e.g. a method is invoked.
http://wwwcs.uni-paderborn.de/cs/fujaba/index.html - OSS - Fujaba Tool Suite combines UML class diagrams and UML behaviour diagrams to a powerful, easy to use, yet formal system design and specification language... The Fujaba Tool Suite RE Edition is especially configured with plugins for Reverse Engineering and Design Pattern recognition.
http://www.jbixbe.com/ - jBixbe gives you a new innovative way to debug Java applications on the conceptual level of the Unified Modeling Language (UML) at which they are designed and makes it possible to find not only simple bugs but also weaknesses and insufficiencies in application design.