Apache Commons offers commons-graph. Under http://svn.apache.org/viewvc/commons/sandbox/graph/trunk/ one can inspect the source. Sample API usage is in the SVN, too. See https://issues.apache.org/jira/browse/SANDBOX-458 for a list of implemented algorithms, also compared with Jung, GraphT, Prefuse, jBPT
Google Guava if you need good datastructures only.
JGraphT is a graph library with many Algorithms implemented and having (in my oppinion) a good graph model. Helloworld Example. License: LGPL+EPL.
JUNG2 is also a BSD-licensed library with the data structure similar to JGraphT. It offers layouting algorithms, which are currently missing in JGraphT. The most recent commit is from 2010 and packages hep.aida.*
are LGPL (via the colt library, which is imported by JUNG). This prevents JUNG from being used in projects under the umbrella of ASF and ESF. Maybe one should use the github fork and remove that dependency. Commit f4ca0cd is mirroring the last CVS commit. The current commits seem to remove visualization functionality. Commit d0fb491c adds a .gitignore
.
Prefuse stores the graphs using a matrix structure, which is not memory efficient for sparse graphs. License: BSD
Eclipse Zest has built in graph layout algorithms, which can be used independently of SWT. See org.eclipse.zest.layouts.algorithms. The graph structure used is the one of Eclipse Draw2d, where Nodes are explicit objects and not injected via Generics (as it happens in Apache Commons Graph, JGraphT, and JUNG2).