Graph Database in Java (other than Neo4J)
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.