PC users have always been able to click on a file in their Save dialog windows and use that clicked filename as the new filename to save as, hence saving over an existing file. OS X never let us do this. But thanks to the new Finder and its Save dialogs, this is possible.
When saving a file, choose a grayed-out file in a folder, and that file's name pops into the Filename field. When you hit Save, the Finder will ask you if you would like to save over top of the current file.

Mac OS X Hints
http://hints.macworld.com/article.php?story=20031012012850181