Apple - How do I merge the tabs of two safari windows when I have more than two open?

First, if the tab bar isn't showing (it usually doesn't show unless there are multiple tabs in the window), select the 1st window you want to merge, then at the menu bar at the top of the screen click View->Show Tab Bar. Next drag the now visible tab bar to the window you want to merge with.

You can drag tabs between windows in safari (I beleive this was added in Safari 4 along with a few other improvements)

If you have many tabs open in a window, it might become hard to drag each of them over. In this case you could bookmark all pages in the current window (Bookmarks > Add Bookmark for These Tabs...), go to the window you want to put these tabs into, and then select Bookmarks > (Folder you put tabs as bookmarks into) > Open in New Tabs.

Do note however that this will cause all of your tabs in the window you bookmarked to be closed. You should only use this method if you are okay with that.