If you are looking for an industrial strength solution, you might consider AppendPDF by Appligent (and/or other products from them). As a command line application, it is very easy to integrate and to run.
Alternatively, there are several libraries (such as iText, pdflib, etc.) which could be used to create such customized documents.
Ah, yeah, and if you want an enterprise product, you might look at the LiveCycle Document Server by Adobe, which is industrial strength, and absolutely viable for this task.