How can I change paper size when using Knit PDF in RStudio?

At least in newer versions of the rmarkdown R package (and Pandoc) you can just set:

---
output: pdf_document
papersize: a4
---

OK, so I figured it out. In the .Rmd file's header, options documentclass and classoption get written into the preamble of the resulting .tex file. The article document class accepts a number of paper size options including a4paper. The header in the .Rmd file will then look something like this:

---
title: "Title"
author: "Name"
date: "Date"
output:
  pdf_document
documentclass: article
classoption: a4paper
---

For more information see: http://rmarkdown.rstudio.com/pdf_document_format.html