Mozilla bug 56690 is working on a way to have the Open in New Window feature open links behind the current window. This is conceptually similar to the tabbed browsing feature that opens new tabs in the background. Jesse Ruderman put together a nice bookmarklet that accomplishes this by simply opening the new window and then bringing the previous window back to focus.
I believe (and Jesse seems to as well) that better behavior is to open the new window behind not only the current window, but also any previously opened windows from that window. This lets you read the windows in the order you clicked them, instead of in reverse order. I tweaked Jesse's bookmarklet to do this. It will cause some window flashing as it shuffles focus, but seems to work.
Open Behind (Moz,IE)
To use the bookmarklet, drag it to your bookmarks or favorites (or copy the bookmarklet code to a bookmark). Go to a web page with links and click the bookmarklet. From then on, all links on that page will open in a new window behind the current window and behind windows opened by clicking the links on the page.
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