I principaly use Evolutionary Computation in Java (ECJ) library for my research because it is, for me, the most documented library I found (a book of 200 pages and 5 tutorials are given). I also used Deap library for teaching.
|Evolutionary Computation Library
| Evolving Objects
Machine and Statistical Learning packages
| Of course, this list is far from being exhaustive.
A recent comparative analysis of Metaheuristic optimization frameworks is available here
A more recent list of softwares are available here