this is really pretty simple. when you move the links and reopen any ID doc, it will pull up a dialog asking if you want to fix the links. point to the new directory where the links for the files are, and as long as they are in the same relational directories they were when you made the file originally, ID will automatically fix all the links for you. in other words, if the images started out in:
user/mac hd/documents/project1/images/
and after your reorganization you moved all the images to
user/mac hd/documents/projects/2008/march/clientname/projectname/images
you can just point to the above directory and it will automatically relink all the images inside that /images/ directory.
where this could get more complex is if you are moving images all over the place. so instead of all the images living in /images/, some are in /dogs/ some in /cats/ some in /people/ etc.... in that case you would need to relink more manually.
like snick said, if you package each ID job before moving your images, the links will all live in the "links" folder of your package instead of somewhere on a drive.