I use the Safari setting (General prefs) of "Open links from applications: in a new tab in the current window", and I just discovered that if you click on a link that is already open, Safari refreshes the page in its tab, rather than creating a new tab.
I suspect that this will work with the "in a new window" setting too, but I thought it was pretty cool!
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Mac OS X Hints
http://hints.macworld.com/article.php?story=20040530023108519