Opening documents such as PDFs in a new window should be automated using JavaScript for the following reasons. Users will often close the web browser when a PDF is opened, mistakenly believing the document has been opened in Adobe Reader, the attribute historically used to open a new window, target, has been removed from the HTML 4.01 Strict specification (it's now deprecated), opening a new window is a behaviour and should be moved to the behavioural layer.

This tutorial is about Windows and JavaScript

With JavaScript you can specify the dimensions, position and visible toolbars of this newly created window, as well as writing code directly into it and having the two windows operating together.

This set of short, easy scripts shows six different ways to close a window from JavaScript, including closing windows from a clicked link, a clicked image, or a clicked form button.

This script produces very application-looking buttons (with an underlined letter) which can be used via ALT key! Works in MSIE, and Netscape.