That way I can have my running programs in the vertical dock not mixed in with my favourite programs.
I shouldn't have to write my favourite programs down on a piece of paper in order to avoid a cluttered vertical dock.
You could simply create a launcher, that had a right click QuickList Menu, that would display and launch all your favourite programs.
You can find examples of the .desktop
entries you will need to make and a general idea here What Custom Launchers and Unity Quicklists are available?