By default (with no way to change it, apparently), Safari will open a new window when opening external application links (like from Mail or TextEdit), instead of reusing the same window or opening a tab. However, if the current tab is blank -- i.e., you've just opened it with no web page displayed -- Safari will use that tab instead of opening a new window. A little bit of a time saver, as opposed to consolidating windows by shuffling around the URLs.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20030310073554655