They both pretty much offers the same service and purpose, i don't see any reason why one would use workdocs over s3.
Amazon WorkDocs is an online document editor and file sharing system. AWS describes it as a "fully managed, secure enterprise storage and sharing service with strong administrative controls and feedback capabilities that improve user productivity."
Amazon Simple Storage Service (S3) is a data storage service. AWS describes it as "storage for the internet".
To give an example:
People would use WorkDocs if they wish to collaborate on documents with other people (eg review documents, add comments, share documents in a team, mount a drive of shared documents). Amazon S3 does not provide those capabilities.