You can place a static text webpart on the master page and set some crazy macro to hide/show or inherit the parent content if you want but I don't think you're going to get what you expecting.
What works well for me is I add the javascript webpart to the master page above the page placeholder and one after. The first one has jquery and anything else that needs to be "first" inline. The last one will have all the other scripts/initializations that need to happen on every page. Then I use the javascript webpart again on the pages you need to add individual/initializations scripts to. With the webpart you can choose where to place the script. It works much better than the static text webpart and is more identifiable.