Well, first of all, the icon that lionel77 uses as his avatar is just the icon for the Finder in Mac OS X. It almost always appears in the dock as the first item. (I suppose you could reposition it within the dock, but it should always be there.) If it wasn't appearing in the dock before, that indicates a bug. From your description, it sounds as if the icon is now appearing detached from the dock and nonfunctional. That also indicates a bug. Neither of these things sounds like a problem caused by aMule.
If I were you, I'd boot from your install CD/DVD and use Disk Utility to repair your boot volume. Then, I'd perform an Archive and Install with Preserve User and Network Settings enabled (use the Options button in the installer). Then, when you restart to your newly reinstalled system, reapply any updates suggested by Software Update. WARNING: make sure you have a good backup. While this procedure should not be destructive to any of your data or applications, you never know. This procedure isn't very complicated, but if you feel unsure of yourself, you might have a professional do it for you.