The following lines from my makefile illustrate two tricks I enjoy.

%.pdf: %.text

pandoc -F pandoc-zotxt -F pandoc-citeproc $< -o $@

%.draft.pdf: %.text

pandoc -F pandoc-zotxt -F pandoc-citeproc --template=draft $< -o $@

(1) Automatically grabbing citation details from Zotero. (2) Using the extension of the requested output file to choose the appropriate template.

Not emacs specific, of course.