As you may already know, OS X lets you manipulate background windows by holding down the Command key—you can drag them, resize them, and more, as long as you hold down the Command key first. You can use this trick, along with a quirk of Safari, to manipulate how links in background windows open.
For instance, say you had two windows open, and noticed a link in the background window that you’d like to read. If you just click the link, of course, the background window comes to the foreground, at which point you have to click the link again to read the article.
If you command-click that link while it’s in the background, it will (as you might guess) load in a new tab. That’s what Command-clicking a link in Safari does, after all. However, what’s somewhat surprising is that the new tab will appear in the foreground window, not the background window—making it easy to read that story you were interested in. By way of comparison, trying this in Camino or OmniWeb will open the new tab in the background window. (In Firefox, Command-clicking on background windows doesn’t work at all.) Not necessarily what you might expect to happen, but quite useful.
If, on the other hand, you want to open a background link in the same tab of the background window, there is a way to do that, too. It does, however, require a bit of mouse gymnastics to accomplish. First press and hold Command, then click-and-hold on the background link you’d like to open. While still holding the mouse button down, release Command, then release the mouse button.
If you did everything in the right sequence, the clicked link will open in the current tab of the background window, leaving your focus on the current foreground window. To be honest, I rarely if ever use this technique, but I do often Command-click background links to read them in the foreground window.