Compressing PDFs containing colour images

PDF Compress, part of the Multivalent PDF tools, really does work well. I used it today to compress PDF files of figures for a paper to be submitted for review (when they don't need the high-quality originals) and it saved about 90%. It's a little tricky to install, but you run it with something like:

java tool.pdf.Compress -jpeg *.pdf

which will compress all the PDF files in the current directory. For line art you probably wouldn't use the -jpeg option, as it doesn't save much over the PDF files that OS X makes anyway.

Then combine the individual files together with Acrobat, or whichever tool you prefer, eg:

java tool.pdf.Merge file.1pdf file2.pdf file3.pdf