ok since it needs explaining
a emulator is a program writen in computer language such as C++ or java the emulator emulates what the acctual console did because the nes is not a computer consold so you cant plug your nes games in to your computer... so you need a emulator to emulate the game just like the nes would...
take your PJ64 that is a computer emulator for the N64 it emulates what the console did...
a java emulator is a emulator be it nes genesis gameboy is a emulator coded in java so it is compatible to be used on a web site.. because websites or not compatible to use C++ or the like...
http://en.wikipedia.org/wiki/Emulator
that was worded badly but you should get the point