Doesn't GOG provide md5 checksums to at least most of its games (the installers, extras don't have them but then you can check their zip file integrity by other means...)?
At least
gogrepo.py is somehow able to get md5 checksums from GOG servers for the games. When you run "gogrepo.py verify", it will check all the GOG game installers in your collection against their md5 checksums. For extras it checks the zip file integrity instead, and for those few installers that don't have md5 checksums for some reason, it merely checks that the size is correct.
On the other hand, if you just need to check that a set of files/subdirectories are identical in two different places, you could also use some small utility like dvdsig.exe or rhash.