Java Clustering Library [closed]

Answer 1

Cytoscape software has several plugins that implement clustering algorithms for networks and numerical data (Nemo, MCODE, clusterMaker, and so on). All plugins are open-source.

Answer 2

There is also ELKI, an open-source university project similar to WEKA, but with the focus on cluster analysis and outlier detection instead of machine learning algorithms. It's pretty advanced, uses index structures for efficiency, and has at least a dozen clustering algorithms.