All we did was write a simple initializer that identifies the OS, copies the proper libraries into place, and then load them before bootstrapping the rest of our application.  If it helps I'd be happy to open source the Platform library I wrote to handle the runtime identification.

Only major downside to this approach is the bloat, since the libraries for all OS's are included in every release.  For us that's an easy tradeoff to keep the deployment as simple as possible and be able to rely on a single runnable jar for windows (as exe wrapped through innosetup), mac (as app bundled), and linux.