I guess I'm just going to filter through the most recent posts and add some suggestions where I can.
The first, and arguably the best fix, is to tell X11 (or XQuartz) to use the Apple command key as a replacement to the Alt or Crtl key. Here's a fantastic tutorial on how to do it: http://hints.macworld.com/article.php?s ... 6110939423
I've been using this method for a while now, and it works most of the time. Of course, it doesn't work when the Mac's default keyboard shortcuts conflict with Gimp's default keyboard shortcuts (as it does in the case of Command-H, which tells MacOSX to hide the windows, whereas in Gimp it supposedly anchors the current layer).
Also, going back to what you were saying, it appears that X11 (and XQuartz) for Mac completely ignore the "Alt" key when using keyboard shortcuts. However, if you DO CLICK on a drop-down menu, you can still press the corresponding key on your keyboard to complete the shortcut.