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.
This project contains Naive and Fishers bayesian classifiers, as described in Toby Segaran's book "Programming Collective Intelligence." The book has python implementations; this is a Java implementation.
Emergent (a major rewrite of PDP++) is a comprehensive simulation environment for creating complex, sophisticated models of the brain and cognitive processes using neural network models.