It's more a question of definition of best emus. I think, that the quality of the emus between the systems is not so different but presentation is. Often the core (CPU, audio, video) can be easily ported to other systems and works fine but the GUIs can't. And coders seem to have a bit of trouble to do a nice, intuitive user interface with QT/GTK/etc or just don't care enough for the unexperienced desktop user.
That's were emus like zsnes with their own softcoded GUIs have advantages. On the other hand development on linux is a lot easier and cheaper with a lot of nice free tools available.
In the end time will tell. But I think the threatenings of M$soft with their upcoming vista/vienna/whatever might give a boost to the whole linux side.