Well, most people complain about HES emulation over-emphasizing the noise channel (thus the percussion), so I'm tempted to choose the odd sounding one as the actual hardware, but that's too easy, so I plugged my Core into the TV and broke out The Kung Fu. Over the puny mono speakers of my TV the noise channel is actually pretty strong (almost dominant, just like the emulators). I also just tested the ROM in Ootake, on all three different modes of PSG filtering.
The 3rd recording is the odd one out and is definitely not original hardware or any of Ootake's PSG modes. I would guess Magic Engine because I think it has the least accurate sound emulation, but I don't know for sure.
The first, second, and fourth recordings all sound pretty similar, actually. It's difficult, at least from the recording, to make out any significant differences between them. I'm not comfortable guessing which is which. I would say that PCE PSG emulation is currently sufficiently accurate that you'd need good equipment and even better ears to really have reason to complain.
It also makes me wonder why anyone would bother, any longer, to pay money for Magic Engine, with such excellent free alternatives available. Yeah, the UI is nice, but it's also custom and doesn't make use of any of the common Windows widgets, which is rather pointless these days.
*edit*
Also, since I'm using a Core I, does that mean I have the "more awesomer" sound hardware that the SGFX supposedly uses?