I've just checked my account at the Nook Store, and so far as I can tell they managed to transfer nearly everything. Not only did B&N get all the DRM-free titles, they also managed to transfer the ebooks in Mobipocket, eReader, and Epub.
Perhaps it would be better to say that they transferred the licenses, because B&N also transferred the many MSReader ebooks I had purchased. Given that Microsoft's DRM servers have long since given up the ghost, that tells us that the actual files were not transferred; just the rights to the files.
In any case, I'm thrilled. I have over 400 ebooks in my Nook account, and that is far more than I ever expected.
How many ebooks did you get?
If you're having trouble accessing the Nook Store, you're not alone. This transfer process looks to be stressing B&N's servers. That should come as no surprise; the transfer is probably increasing the number of transactions in the Nook Store by a significant multiple and there's little you can do except wait for the situation to settle down.