If the Bookmarks.plist has been overwritten for some reason, the bookmarks are gone. Safari does not automatically back up the file. Backing up data on a computer is very important just for this kind of event.
At least for bookmarked sites you have visited recently, you can look through your History to revisit sites to make new bookmarks. You can also use the free utility
Retrospective to search through Safari's cache to see if any of the address are there. You would then have to copy the address from Retrospective and paste it into Safari's address window and then make a new bookmark.
For the future, you can manually back up your bookmarks. Go to /users/user name/Library/Safari (the Safari folder in the Library folder on your Finder's Home page) and click on Bookmarks.plist to highlight it. Now press Command-C to copy the file. Go to any other folder and press Command-V to copy the file in that location. If you ever need to restore your bookmarks, you could then move this copy (or a copy of the copy) back into the Safari folder. (You could copy the plist in the same folder - the name of the copied file would be Bookmarks copy.plist)
This trick will also work for your History.plist file if you wanted to save your history list.
