There are tools that can compare two databases in great detail, but the caveat I found, it is that they can only compare two databases, so while they’ll be fine to compare DEV<=>PROD or QA<=>PROD, they’re not a good fit to compare and find the differences in, literally, thousands of databases
There it’s where I was, so after some time trying to postpone the inevitable, it was time to roll up my sleeves and get the job done.
Click through for Raul’s explanation and process. At one point, I’d written something which used Red Gate’s Schema Compare DLL to do something similar. The big problem you run into is when there is no single, canonically correct database and you’re trying to generate one from the tangled mess of objects.