Missing photos from iPhoto
The 3rd party software may scan the raw data for photo files and identify them by whatever signature it may find (JPEG or other). Mac OS X doesn't come with that feature since it naturally assumes the file system will work correctly and it does everything thru the file system. Data recovery software just isn't a standard feature of an operating system.

PhotoRec is a well-known multi-platform software that would probably be able to help in your case and is free/open source if you want to try that. http://www.cgsecurity.org/wiki/PhotoRec
"PhotoRec ignores the file system and goes after the underlying data, so it will still work even if your media's file system has been severely damaged or reformatted."

Be aware, the more you write data to your hard drive, the more chance the underlying data that might be recoverable will be destroyed by overwriting. The best way to do it would be by removing the hard drive and using it as a secondary drive to another computer that's running PhotoRec to completely minimize the chance of overwrite damage.