n64 emu plugins have a ".dll" extension and usually will reside in the "plugin" subfolder of the n64 emulators' directories. In a perfect world, all plugins are interchangeable with other emulators that share the compatibility spec. In the real world, not all work in all emulators.
As far as I know, all graphics plugins are now completely cross-compatible.
However, Jabo's audio plugin for instance, will work in pj64 (which is what it was designed for), but will not work in 1964. The reason for this is technical, so here it goes: it is because 1964 doesn't do a certain type of emulation (low-level-emulation of the rsp).
So basically, you take the dll file and put it into another emu's plugin folder..then you can select it from an options window located somewhere in the emulator.