Yes, at least three come to mind (partly copied from my own answer at https://softwarerecs.stackexchange.com/a/31158/22778):
pdftk
That is the tool I use for larger PDFs and bulk operation. It's great for splitting, concatenating and rotating PDFs. I use krop (see below) for cropping.
https://www.pdflabs.com/tools/pdftk-the-pdf-toolkit/
Install with apt-get in Linux:
sudo apt-get install pdftk
It is also available for Windows (thanks to @MrWhite).
pdfcrop
Checked out pdfcrop: http://manpages.ubuntu.com/manpages/gutsy/man1/pdfcrop.1.html
It is described in more details here: https://askubuntu.com/questions/124692/command-line-tool-to-crop-pdf-files
krop
krop is what I love to use: http://arminstraub.com/software/krop
I use the GUI, but it can be run via CLI as well - maybe that is what you are looking for:
:~$ krop -h
usage: krop [-h] [-v] [-o OUTPUT] [--rotate {0,90,180,270}]
[--whichpages WHICHPAGES] [--initialpage INITIALPAGE] [--autotrim]
[--selections {all,evenodd,individual}] [--no-kde] [--no-PyPDF2]
[file]
krop: A tool to crop PDF files
Copyright (C) 2010-2015 Armin Straub, http://arminstraub.com
positional arguments:
file PDF file to open
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
-o OUTPUT, --output OUTPUT
where to save the cropped PDF
--rotate {0,90,180,270}
how much to rotate the cropped pdf clockwise (default: 0)
--whichpages WHICHPAGES
which pages (e.g. "1-5" or "1,3-") to include in cropped PDF (default: all)
--initialpage INITIALPAGE
which page to open initially (default: 1)
--autotrim create a selection for the entire initial page minus blank margins
--selections {all,evenodd,individual}
to which pages should selections apply
--no-kde do not use KDE libraries (default: use if available)
--no-PyPDF2 do not use PyPDF2 instead of pyPdf (default: use PyPDF2 if available)