In our office, we have to scan a bunch of incoming documents every day. We do have a scanner with an automatic feeder which will save each scanned document to some fileshare on our network. Yet someone has to stand in front of the scanner and feed it one document at a time, wait for the scanner to finish and upload, then feed it the next one to make sure we get one PDF per document in the end. (Each document may be one to X pages.)
So the idea would be to have a kind of separator page which can be put into the pile between the documents, then scan the whole pile in one goal. After that we would need a tool to split the resulting huge PDF into the individual documents again and we don't want to do this manually. It shouldn't be rocket science for some batch pdf processing tool to recognize the separator page and split the PDF accordingly.
The next step would be to use separator pages which would tell the tool into wich folder the next document has to go, like "invoice", "customer enquiry", ...
I hope I explained well what I am looking for? I am surprised I did not find anything, at least not using freely available tools such as PDFtk or the like.