Java2 can run natively on FreeBSD but you have to download the source code from Sun then applying some patches you can find on the Java FreeBSD page (look at www.freebsd.org
in news section to find the Java news). But remember that this support is not supported by Sun and is in development state.
For the question of speed between Linux and FreeBSD, last year (or the year before), a serie of tests showed that Quake Arena was as fast on FreeBSD through Linux emulation as on Linux. If you used Netscape one day on FreeBSD, it was under Linux emulation and worked perfectly good (as Netscape could).