Kiss FFT is a small and simple FFT library. It has no complicated platform-specific optimizations, can do either fixed or floating point with just a recompile, and is efficient enough for all but the most demanding applications.
AIOTrade is a free, open source stock technical analysis platform built on pure java. Its pluggable architecture is also ideal for custom features extending, such as indicators and charts. It Requires JRE 1.5.0+.