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.
This may not help you at all, but there a program called Dockless that allows you to hide an application from the Dock. Unfortunately, I think it hides the menu bar too. Depending the exact situation, this may or may not work for you. Hope it helps though!
Best Answer
Go to System Preferences → General and disable ‘Allow Handoff between this Mac and your iCloud devices’.
This feature is called Handoff, part of Continuity. You can read more about it in the Apple KB: