In an update to a previous post, you can add a frame to your 4×4 handouts as follows:
[~]$ pdfnup --frame true --nup 2x2 cfd3_design.pdf
worked very nicely for me! In a change from previous behaviour on Ubuntu 12.04 this now comes out as:
cfd3_design-nup.pdf, but the original file remains in place.