More and more, I have to mess with bunches of pdf documents.
One way is to automate Adobe Acrobat which comes in multiple versions. This usually means writing Adobescript javascript routines for the version of acrobat being used and then calling them from the outside ie. Macro Scheduler, using a method I described previously in this forum.
Another way that avoids Acrobat is to use the free iText pdf libraries available (use google to find) but this means writing everything in Java.
I've stumbled onto a very nice, free (GPL) command line program here: http://www.accesspdf.com/pdftk/ that is based on the iText libraries and is easy to call from Macro Scheduler. It merges, splits, encrypts, decrypts, repairs, and fills forms for pdfs. A sample pdftk command line call could look like:
let>TheCommandLine=pdftk 1.pdf 2.pdf 3.pdf cat output 123.pdf
Let>RP_WAIT=1
Run Program>TheCommandLine
to join three pdf files into one.