One of the cool things about Adobe's PDF stuff is that you can create customized "presets" for generating PDFs. This is basically a "recipe" that ensures the resulting PDF meets the specs you need, and these presets are actual file plug-ins that can be sent to clients to install on their computers. Once installed, they can generate a PDF using that recipe and the resulting PDF file will conform to what you need. We use a few specific printers for all of the stuff we create at my office, and most sent us their PDF presets to install (the others just told us to use a certain built-in preset). For us, and the advertisers that send us tons of ads, that's eliminated 90% of the headache of missing fonts, RGB instead of CMYK, etc.
Here's an (ugly) link to some info that might help you if you wanted to create your own:
http://help.adobe.com/en_US/Acrobat/9.0 ... f10.w.html
Two years ago, I moved the magazine I publish from Quark to InDesign for many reasons, but one of them was definitely the integration of page layout with PDFs, the way the print industry has moved. For what it's worth, ID definitely makes handling/generating PDFs much easier, as Thorz indicates, and even though it's not easy and an investment, I don't hesitate to suggest switching from Q if it's a possibility at your office. I've never been an Adobe fan at all, but their CS bundles are great for commercial designers and publishers.