Note 2: If the paper isn't here, look in ocharles' git-annex repository. robbinch's Papers git repository may also contain what you're looking for.
I use k2pdfopt to turn the typical 2-column papers in PDF format into a PDF suitable for an e-reader. It seems to handle figures well, too, so I'm happy with it.
I've also taken some of the single-column papers with huge margins and ran them through the tool to make the font bigger on an e-reader.
I use the GUI on Windows (in administrator mode) to generate the PDFs, but here are the command-line options:
-dev kbhd -mode 2col -c -om 0.2
This takes a 2-column paper and generate a PDF suitable for a Kobo Aura HD and sets a 0.2 inch margin around the document. Here's an example:
