pdfcrop (commonly included with LaTeX) for cropping margins - it cuts the pdf down to its contents then adds a margin of your choosing, extremely useful for forcing academic papers to have consistent margins, pdfcrop --margins 72 *pdf here* will create a document with a ~1in margin all around (it uses bp as its units)
vips for resizing/converting images - it's a bit faster and lighter than imagemagick in my experience, although the main reason I use it instead of imagemagick is just because I like playing around with stuff I haven't used before :) It has an officially supported python binding too