And just in case you don't already know, to see the hidden folder ~/.aMule, use the Go to Folder command in the Finder's Go menu. Enter ~/.aMule into the dialog.
Another thing to try besides what Kry said: check aMule's dock menu. Ctrl-click on aMule's icon in the dock. It should present the names of the window ("amule"), as well as several commands. Select the window and it might force the window to be visible.
Or, use Exposé to find aMule's window. Use F9 to see all windows and select aMule's. Alternatively, with aMule as the active application, use F10 to see just its windows.