There is one big issue for me with Dock in OS X - it does not shows you if more than one window is open in an application.
For example, I'm browsing with Firefox and a site opens a background window with some sounds - and I have no idea where it comes from. The dock does not tell you if some application opens more than one window...
Is there a way (or some application) that can add some mark to application icon in Dock if it has more than one window open?