• Preferred apps and currently running apps are interspersed on the dock.
• Forced centering of the dock removes any opportunity for muscle memory. (Thanks, Dan.)
• You can't assign keyboard shortcuts to preferred apps.
• There are no keyboard shortctus for selecting and opening minimized windows.

Here's a solution that addresses all of these issues and works quite well for me. Take a look at the bottom portion of my PowerBook's screen:

On the left, you see preferred apps. On the right, you see running applications, minimized windows, and the trash. Icon magnification is turned off; the same screen real-estate is always occupied.

The leftmost dock is a DragThing dock with background transparency. The rightmost dock is the Apple dock, hacked significantly and locked to the bottom corner of the screen by TransparentDock.

I've removed all "preferred app" icons from the Apple dock. If no apps are running, the dock on the right displays only the trash.

I've also used DragThing to assign hotkeys to my preferred apps. These hotkeys are as useful for opening apps as they are for foregrounding them.

To get keyboard access to minimized windows, I turned on System Preferences → Keyboard → Full Keyboard Access. (Thanks, Yoon Ha Lee.)

Keyboard access can be used for application switching, but Command-Tab is still my preference since it avoids alternating between minimized windows. Because the dock only displays running apps, the cognitive overhead of Command-Tab is reduced.

Do you have any thoughts on making the dock better? Drop me a line: web (at) delver (dot) org.