I prefer LibraryThing to Goodreads because LibraryThing focuses more on cataloging than social features. Their team also builds software for actual libraries. They source book data from almost 5,000 external sources so it's easy to map ISBN information with the correct edition and cover. You can also get your data out pretty easily, they offer exports in multiple formats.
EDIT: For most books, you can scan the barcode on the back to get the ISBN. Mass market paperbacks seem to usually have separate UPCs. The ISBN barcode is often located on the reverse side of the front cover, so you want to scan that one instead of the one on the back.