As RobV said, if your graphs can be represented in just about any custom format such as RDF or DOT language, you're in luck! Here's various options you have:
- RDF: Jena - Considered to be the de facto implementation of RDF for Java, however it has it's oddities such as heavy usage of Iterators.
- RDF: Protégé - If you don't use Jena (and even if you would) but would like to use RDF, Protégé is the tool for you. It's basically a really well done ontology editor which makes handling the graph data a breeze. It also uses a plugin hierarchy similar to Eclipse and there's loads of plugins available so you can plugin stuff like OWL ontologies easily.
- DOT: GraphViz - Another very popular tool, GraphViz can generate graphs from DOT language. Very powerful, a bit tricky to learn but also potentially all you need.
Of course if it fits your company's profile, you could develop your own and start selling it as a product.