SIMBRAIN is a free tool for building, running, and analyzing neural-networks (computer simulations of brain circuitry). Simbrain aims to be as visual and easy-to-use as possible. See our design goals. Unique features of Simbrain include its integrated "world components" and its ability to represent a network's state space. Simbrain is written in Java and runs on Windows, Mac OS X, and Linux. Click here for a video introduction to some of Simbrain's features, check out the screenshots, or just download the software and start experimenting. Simbrain is open source, and constantly evolving. We'd love for you to join our team. To discuss any aspect of Simbrain check out the forum.
Neuroph is lightweight Java neural network framework to develop common neural network architectures. It contains well designed, open source Java library with small number of basic classes which correspond to basic NN concepts. Also has nice GUI neural network editor to quickly create Java neural network components. It has been released as open source under the LGPL license, and it's FREE for you to use it.