It is highly improbable that you will find such a (commandline) tool. However, there are tools partially do what you request.
Likely you have an original PDF and you want to create a new PDF using your logo and (most of) the content from the original PDF.
In that case it might be smarter to rethink the order in which you want to do things.
01.) It would be better to first extract the content from the original PDF to file(s) in a separate folder:
http://pdftohtml.sourceforge.net/ 02.) Again using a different (sub-)folder to strip the html content, leaving you with text file(s) only:
http://kmachine.home.xs4all.nl/html2txt.htm03.) Use a graphical editor in cli mode to resize/crop and save graphical content from step 1:
http://gd.tuwien.ac.at/graphics/xv/html-docu/command-line-options.html04.) Using a text editor in cli mode to store the differences between HTML content and the stripped text (to retain a simple HTML layout):
http://sed.sourceforge.net/ (this appears to be the most capable text editor for command line operations)
05.) Using a text editor in cli mode to replace desired specific content inside the stripped text:
http://sed.sourceforge.net/ 06.) Using a text editor in cli mode to store the content from step 4 into a previously created HTML template (with your positioned logo):
http://sed.sourceforge.net/ 07.) Using a text editor in cli mode to store the content from step 5 into a previously created HTML template (with your positioned logo):
http://sed.sourceforge.net/ 08.) Using a text editor in cli mode to store the content from step 7 in a different (sub-)folder as HTML file(s):
http://sed.sourceforge.net/ 09.) Convert the HTML file(s) to PDF:
http://code.google.com/p/anytopdf/ - uses the OpenOffice/LibreOffice (portable version) PDF conversion capabilities (which are awesome in my point of view)
10.) Cleanup the mess created during the conversion process from your hard drive:
Use a BATCH script or something similar
All the above is great on simple PDF's, if you have to use complicated PDF's (heavy on layout) you will have to do things manually as preserving the layout will be practically impossible when automatizing.
Have fun puzzling with the command line options of each and every tool...