If you want a free tool with GUI to crop a PDF file under Ubuntu, then I recommend that you try PDF Quench, which is simply a tool written in Python used under Ubuntu to crop PDF documents by eliminating unnecessary spaces.
To install PDF Quench under Ubuntu 11.10/11.04, open the terminal and run these commands:
sudo apt-get install python-pygoocanvas python-poppler python-pypdf
wget -O pdf-quench_1.0.0_all.deb http://goo.gl/AJrS3
sudo dpkg -i pdf-quench*.deb
You can then start it via the Unity Dash.