In Lion, Finder allows you to do what you’ve never been able to do before. No, not leap tall buildings in a single bound. You can now merge the contents of two folders of the same name without having to sacrifice/overwrite one.
In previous versions of the OS, your options were either Stop or Replace (or similar, depending on your version). In Lion, you’ll now see a third option in the popup window, Keep Both, and a list of unique files it finds when comparing the two.
Important: This will only work if you use Copy (Command-C) and Paste (Command-V) to merge the folders. I’m not sure why it works this way, but take heed, as the drag ‘n’ drop method will only show the Stop and Replace options of OS versions past…