I have been using LaTeX for a while now and I have always been annoyed by the fact that I have to run the pdflatex command multiple times to get the references and the table of contents right. Today, I colleague of mine told me about the latexmk command. It is a tool that takes care of all the dependencies and runs the necessary commands to generate the PDF file.

You can run:

latexmk -pdf yourfile.tex

And it will take care of everything. It will run pdflatex multiple times if necessary, it will run bibtex (or 'biber', as in my case) if you have a bibliography, and it will generate the PDF file.