Oh thats going to stir this one up.
In my opinion JIT is a form of emulation.
After all, you translating non-native code to PPC instructions.
Its all emulation, as I said earlier. Java "emulates" machine language, which at some point is compiled down to bytecode. Just like C, or even assembly at some level. These are all abstractions on top of the hardware. When mac went PC, did anything really change about the experience or the look and feel? No. The abstractions that made an Apple an Apple were still there, they were just being implemented differently on the hardware. Thats why the morphOS people say its Amiga "done right". They understand that hardware evolves, but the OS can stay similar to previous OSes and still be called what it is. If I run OSX on a hackintosh, I am running a mac. If I run morphOS on a PPC macmini, I am running a next gen amiga-like OS. Similar if I were to run NetBSD on PPC/ARM/IA64/SPARC/X86/X86-64/Amiga/VAX/DEC etc etc etc ad nauseum. These are all emulation layers on hardware architectures. On the way down to the actual logic, you are removing layers of abstraction (layers of emulation) until you finally get to the 3.3 or 5v signals that make up the real computer.
so for the tl/dr crowd: emulation is simply another abstraction layer in a ginormous soup of abstraction layers.
The only thing that runs "natively" is a bitstream.