dockmacos
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?
You can put
read -p "Press Return to Close..."
as the last line of the script. That will keep it up until you hit enter.
Re: your edit
If you invoke bash (or whatever shell you use) as the last line of the script it should (as in does for me on Linux) stay open with a prompt.
Try unchecking the checkbox at the bottom in System Preferences » Exposé & Spaces.
Remember to set your browser to open links in new windows instead of new tabs of existing windows.
Best Answer
The short answer is that there doesn't appear to be anything built into the system which accomplishes this goal.
This is not to say the goal is impossible; there are addons like Docktopus which are able to dynamically "badge" Dock icons. Thus, there is obviously some form of programming interface to the Dock which may make it possible to develop a solution, if you're inclined to software development.
After scouring Google, the only app I found which dynamically badged Dock icons on Mac OS X was Docktopus, and this is sadly not one of its options. So I think your short answer will remain, "no," for some time, again, unless you build your own. Sorry. :(