I've just starting using Vectorz, and it's great. Fast, in-place transformations, readily available from Maven Central, well documented.
From the README:
Fast double-precision vector and matrix maths library for Java, based around the concept of N-dimensional arrays.
This library is designed for use in games, simulations, raytracers, machine learning etc. where fast vector maths is important.
Some highlights:
- Vectorz can do over 1 billion 3D vector operations per second on a single thread.
- Specialised matrix types for efficient optimised operations (identity, diagonal, sparse etc.).
- Support for arbitrary n-dimensional numerical arrays.