When I travel around the country and speak at events, one of the topics I cover is usually an in-depth understanding of how Adobe's transparency model works. One of the nice things about what Adobe has done with the Creative Suite is that they have made this transparency model a core technology which is shared across the applications. So what you learn about transparency can be applied to Illustrator, InDesign, and Acrobat.
To help people achieve the best possible print results from their files, I have created a small checklist, which I have published as a small card (I hand these out at events, such as at the recent Creative Suite Conference in Chicago). Knowing that I can't possibly visit each person individually (although that would be really nice!), I've made the file available for download here (PDF 68k).
Detailed information about transparency and PDF/X-1a can be found in Chapters 11 and 12 of Real World Illustrator CS2.