It's Time To Move On Folks
Listen, the whol idea of the dock is getting outdated anyway. Especially placing folders in it. I know it's hard when you have to give up an old habit, BUT IN THE END IF YOU REPLACE THAT HABIT WITH A BETTER WAY OF COMPUTING, IT'LL BE A BENFIT TO YOU.
I seriously suggest you all take a look at Quicksilver. It is a far superior, and far more advanced way to call up files, folders, and especially apps, you can even manipulate quite powerfully the files inside of quicksilver. Like find a file anywhere zip it and e-mail it all with a few quick key presses never leaving Quicksilver. And it's pluginnable! I suggest you all ditch your application folder in the dock approach and start quicksilvering. It's smart too, it starts to learn which things you open the most and makes them even quicker to get at. For instance, I open firefox all the time, so now if I just type an "f" and hit return firefox pops right up! If you use the "bezel" display look, you get huge tasty icons as a great visual feedback.
Truly guys, use stacks for what it's great for, quick, transient organization without cluttering your desktop, it's like a hidden desktop. And use quicksilver for everything else! you could even use spotlight for all that, it's just not quite as fast as QS. HAPPY LEOPARDING!