We've been using md5summer on Windows, which works great for pointing at a folder, generating MD5 hashes for all files and then comparing against the migrated copy.

Any idea what purpose including an MD5 Sum file within a zip file that you're downloading serves? I understand the algorithmic checking to make sure the file hasn't been modified. But I just ...

If two files have the same MD5 sum, the files are exactly alike - which is why MD5 "fingerprints" can verify whether or not your downloaded file got corrupted in transit.