There's only one major difference, but it's a doozy; Save and Compact basically saves a new version of the file under the same name while deleting the old version. The point of this? To optimize the file by stripping out all extraneous information, such as change/undo histories. This can significantly reduce the size of the file saved on your hard drive.
Be warned, though: Save and Compact is a double-edged sword. With your original file deleted and you change/undo history gone, you can't backtrack over anything you might have done.
