You have the choice to start Jake2 with jogl OpenGL driver and joal OpenAL driver or to use lwjgl as OpenGL and audio library. The lwjgl version has the advantage of better fullscreen support especially on linux and it is slightly faster than jogl. But there are still some keyboard issues with the lwjgl version (deadkeys and repeats are not handled properly). So try out both versions and use the one you like better.
The webstart version runs on Linux, Windows and Mac OS X (Intel/PPC). Special thanks goes to Kenneth Russell for his generous Mac mini sponsoring.
Please send feedback to our Jake2 forum at sourceforge.