Here are a couple of website examples:
Is this simple or difficult coding? Can this be accomplished with fpdf?
Depends how you handle it.
I would suggest just using pdftk on the server to merge the files, and send them to the client for downloading.
I don't know if fpdf can do this. But if you are doing this on linux you could just make your script use ghostscript to merge the files uploaded. It would be something like
gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=out.pdf uploaded1.pdf uploaded2.pdf
It looks like the website SimplyPDF.org is a startup which is going to offer exactly what you need. However, they seem to be in the process of creating their website.