The GNOME printer dialog will let you do this, but that's not helpful unless you're using Linux :-) CorelDRAW has a beautiful imposition tool, and you can embed PDFs in your documents. CutePDF Pro (Windows only) has a pretty decent PDF imposition tool, although I don't find it as elegant as CorelDRAW.
And for basic, bare-metal, command-line PDF imposition, I use
pdfnup from the PDFJam project (UNIX, Linux, and Mac OS X only, sorry). An example I use often (a two-page 4¼×5½" PDF, imposed four times onto two 8½×11" pages):
pdfnup --paper letterpaper --nup 2x2 input.pdf '1,1,1,1,2,2,2,2' --outfile output.4up.pdf --no-landscape
Looking at each argument:
--paper letterpaper specifies the paper size, of course
--nup 2x2 says I want 4-up in a 2×2 grid, of course; you'd want
--nup 3x3 instead
input.pdf the two-page input file
'1,1,1,1,2,2,2,2' the layout of the pages -- so I want each of the four copies on page 1 of the output file to be from page 1 of the input file, and so on
--outfile output.4up.pdf the name of the imposed file
--no-landscape pdfnup tries to do imposition intelligently, but sometimes it comes up with idiotic arrangements. For me it shrank the pages (something you may want with your 3×3 layout, but I definitely didn't) and put them into the middle of a landscape page. This option forced it into portrait.