We prefer to receive Mac-based files (OS X) and run all the latest standard production software including Macromedia Freehand MX, Adobe Creative Suite and Quark Xpress.
Our systems utilise a PDF workflow and we have all the necessary software to trap, impose and RIP PDF files.
It is important that any PDF's supplied to us for output are constructed correct and accurate.
Transparency
If you're using transparency effects (lens fills, drop shadows, blending modes, etc) consider the stacking order (the top to bottom order of objects on a page) because the order affects which objects are flattened. Whenever possible place text and line art elements above all objects with transparency effects to minimise the chance that the flattener will process them.
Let us know if you have used transparency effects so we can verify that it will print as expected.
For more information on this see Adobe's website or download this PDF.
There is also this PDF: A Designer's Guide to Transparency for Print Output.
Guide to creating PDF's
Follow this link for instructions on how to create quality PDF's for printing.