A web site should never force new windows on users. If it is necessary as exception to the rule, target="_blank" is the method to use. JavaScript's window.open does not send information about the referrer.
Many web designers find it natural that some links open web pages in a new window. External links is the most obvious case. It is even considered to be great usability, because it is an intuitive way to mark that the user is leaving one web site for another one.
It also seems natural that some internal links open as new window. The new window can even be reduced to a bare frame without the menu line and the address line of the browser. A word list, a help function, a form asking the user for some input, user-friendly version of a page, tip a friend by email, etc.
It is often said that new windows are bad for beginners and good for advanced users, and that we have a schism between common sense accepting new windows as a matter of fact, and experts of usability regarding new windows with contempt. It is to simple analysis.
It is about something else. Who should open the windows? Is it the user, or is it the author of a web page. There are four solid arguments against forcing new windows on the user.