Restrain your users from uploading files extensions that you do not wish to accept. For each document types, you can select a limited amount of accepted "mime types".
Some of your users might be uploading files such as images that you would like to be converted in other extensions; for example .pdf.
Let's say you request multiple pages that you want to be automatically merged in one single document. Choose the document types to be merged and let the magic happen.
Want to get some specific documents renamed according to your internal nomenclature? Get it done choosing prefixes per document types. You can also add your user's internal ids to rename documents.