You can actually run WinUAE under WINE if you like, but I found that the interface can be flaky. Depending on your version of the latter, your mileage may vary - hopefully better. On my system, for instance, if you use F12 to bring up the WinUAE interface, it can refuse to close again as if the keypress event wasn't consumed. Opening it from the windows systray (under gnome, it puts this icon in your notification area) works fine though.