I'm appending my papers to my thesis using the pdfpages package as so
\includepdf[pages={-}, addtotoc={1, chapter, 1, Paper 1, paper1}]{paper-1.pdf}
Can I modify the layout of paper-1.pdf such that two pages per sheet are printed?
As mentioned by JLDiaz, you should use the nup option. According to the pdfpages documentation, the syntax of the option is: nup=(xnup)x(ynup), where (xnup) and (ynup) specify the number of logical pages in horizontal and vertical direction. You may also want to use the landscape option in order to switch to landscape orientation and avoid twisting the neck of whoever wants to read your document on screen!
\documentclass[twoside]{article}
\usepackage{pdfpages}
\begin{document}
\pagestyle{plain}
\includepdf[pages={1-8},nup=1x2,landscape=true]{tb88flynn.pdf}
\end{document}
I've printed the output to check that everything prints with the desired orientation. If you select "left bind" as binding position (or something like that) in the setup of your printer, you'll get this (after binding):

tb88flynn.pdf is available here.
+90 makes more sense. This way, if you have your two-side document open in front of you, you can just rotate it by 90 clockwise and you'll be able to read 4 logical pages like so: 1 (Left up), 2 (right up), 3 (left down), 4 (right down).
– jub0bs
Mar 27 '13 at 22:57
status-lua.pdf out of the box rather than referring to an external file.
– kiss my armpit
Mar 28 '13 at 00:15
nup=2x1. It is in the manual, which is worth reading, since it describes lots of options to customize the layout. – JLDiaz Mar 27 '13 at 10:13