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Quite a hard question to phrase but I know there is an Applications folder in the Dock, above that being programs pinned to the dock, with a dot showing that they are open.
Is there a way to organise these pinned applications into folders on the dock (such as 'Word Processing', 'Development' etc) so clicking the folder shows the apps inside and gives it focus when its open and the window is minimised the icon within that folder? So instead of having like 20 apps on the dock, you have 3 folders, with the apps inside?
See Daniel's answer. One other option is to look into software like Alfred, LaunchBar, Quicksilver, or Google's Quick Search Box. Acting like spotlight on crack, they let you quickly launch applications from a hotkey followed by a few keys of the app's name, allowing you to quit apps and leave them unpinned from your dock, rather than merely closing them, yet still have them just a couple of keystrokes away. – peelman – 2011-03-03T00:21:49.160