yEd is a very powerful graph editor that is written entirely in the Java programming language. It can be used to quickly and effectively generate drawings and to apply automatic layouts to a range of different diagrams and networks.
DotML is an add-on for the 'Dot' graph drawing tool from the AT&T GraphViz software package. It allows to specify 'Dot' graphs in an XML syntax, which then can be transformed using XSLT to the native syntax that is understood by the 'Dot' tool.
APIviz is a JavaDoc doclet which extends the Java standard doclet. It generates comprehensive UML-like class and package diagrams for quick understanding of the overall API structure.