If you are starting with Neural Networks you should check out my online book on the subject. It contains over 300 pages of information on Neural Network Programming in Java. You can access it here.
G. Ruß, R. Kruse, M. Schneider, and P. Wagner. Artificial Intelligence in Theory and Practice II, volume 276 of IFIP International Federation for Information Processing, Springer, (July 2008)
G. Ruß, R. Kruse, P. Wagner, and M. Schneider. Advances in Data Mining (Proc. ICDM 2008), page 47--56. Berlin, Heidelberg, Springer Verlag, (July 2008)