Winmerge is fantastic as long as the directory structures match up. It doesn't remove empty directories by default, so you'll need to play with the settings or use something like Remove Empty Directories to clean them up.
Yet Another Duplicate File Remover or Fast Duplicate File Finder will let you track down all the remaining duplicates. The latter allows better controls for determining which directory files will be left in, however, only Winmerge and YADFR seem to cache the file hashes so subsequent searches are way faster in those apps. Also, watch out for optional tool bars if you install Fast Duplicate File Finder as it is the free version of a commercial product.
I had to backup all of my files to an external drive to switch laptops and I know that I have tons of copies of my older files that I've backed up several times. Does anyone have a good program that I can scan my files with to find duplicates so I can condense my file stash?