Wandora is described as 'general purpose information extraction, management and publishing application based on Topic Maps and Java'. There are more than 10 alternatives to Wandora for a variety of platforms, including Windows, Linux, Mac, Online / Web-based and iPad. The best alternative is Gephi, which is both free and Open Source. Other great apps like Wandora are Cytoscape (Free, Open Source), Polinode (Paid), KeyLines Graph Visualization Toolkit (Paid) and Linkurious (Paid).
Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of plugins are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.
Polinode is a tool that makes it easy to perform powerful network analysis. You can either upload your own network data or use the integrated relationship-based survey tool to collect data for you before analyzing and visualizing your networks.
Linkurious provides a graph visualization and analysis platform used for fraud detection, anti-money laundering, intelligence or cybersecurity. Easy to deploy and highly extensible, Linkurious Enterprise makes it easy to uncover insights hidden in complex connected data.