I thought that only pdftk was good for fiddling with pdf files, and struggled for porting it (but with no joy, because a java compiler was needed, which lacks).
But I discovered I could do the same thing with pyPdf. Here is a quick howto:
1) install python and python development packages as described in http://pymaemo.garage.maemo.org/manual_installation.html
2) download pyPdf from http://pybrary.net/pyPdf/
3) uncompress than install while being root:
python2.5 setup.py install
4) now you can cut, join, encrypt, decrypt, rotate, crop pdf files, and apply watermarks, as described in the pyPdf page (see examples). You can use the python command line, cutting & pasting & editing the example commands, or write a script.
Or, some pythonologist could code a GUI for that, maybe.

I am very happy with it. My aim is using my IT as a notebook replacement, and this is a nice step forward