What are some considerations in organizing apps in the dock?
There are lots of little application launcher utilities available, to name two Overflow and the venerable DragThing.

Personally, I prefer keyboard-based launchers like Alfred or LaunchBar.

OS X Lion will have feature called Launchpad which looks like it will be a good replacement to the dock for launching applications.

Organizing Apps in the Finder or launching them all via the Dock is rather futile, in my opinion — unless you have a very small collection of Applications…

If you're looking for folder icons, there are tons of online sources. I recommend the Iconfactory to start. 

Customization: in the Finder if you use the Command Get Info in the file menu on a selected folder (also available in the right-click contextual menu), you can select the icon in the info window top-left. From there you can copy the icon resources and paste them.

So that's how you can customize the folders, copy icons from a downloaded folder source, and paste them into your new folders. Panic software produces an excellent Application for icon management that can also streamline this process called CandyBar.