The problem I've noticed with WinUAE (though I haven't tried any hardware emulators yet -- intending to get the Replay) is that there is an input (or maybe it's really output) delay that doesn't quite seem to cut it. From pressing a button or moving the mouse to the change actually showing on screen takes some time (longer than on real hardware). Some of the immediacy on the real hardware is lost, especially in games that use the mouse.
Software emulation is also a huge waste of energy.
