For rendering and converting documents there are three commands available:

mutool draw
This is the more customizable tool, but also has a more difficult set of command line options.
It is primarily used for rendering a document to image files.
mutool convert
This tool is used for converting documents into other formats, and is easier to use.
mutool trace
This is a debugging tool used for printing a trace of the graphics device calls on a page.

There are also several tools specifically for working with PDF files:

mutool show
A tool for displaying the internal objects in a PDF file.
mutool extract
Extract images and embedded font resources.
mutool clean
Rewrite PDF file. Used to fix broken files, or to make a PDF file human editable.
mutool merge
Merge pages from multiple input files into a new PDF.
mutool poster
Divide pages of a PDF into pieces that can be printed and merged into a large poster.
mutool create
Create a new PDF file from a text file with graphics commands.
mutool sign
List, verify, and sign digital signatures in PDF files.
mutool info
Print details about objects on each page in a PDF file.
mutool pages
Print details about media box, artbox, etc for each page in a PDF file.

And finally, there is a tool for doing anything you can imagine:

mutool run
A tool for running Javascript programs with access to the MuPDF library functions.