Merge PDF annotation
You can do this simply with Adobe Acrobat Professional. I tested this with Acrobat Professional version 8.3.1 on my Mac OS X 10.5.8 system.

Pick one of the annotated files to aggregate the comments. Open it with Adobe Acrobat Professional. For each of the other files, select the menu command Comments... Import Comments..., and from the resulting File Open dialog select each of the other files in turn. Acrobat will read the comments from the selected file and place them into the first file. A Comments List opens at the bottom of the window, showing all the comments in the document.

You now have a PDF file with all the comments in it. Save it under a different file name, and carry on with your work.

Note that you make this much easier for Acrobat if everyone marks up the same PDF file. Acrobat can import comments from one version of a document to a different version of a document, but it the comments won't always end up in the right place. The menu command Comments... Migrate Comments... is intended to help you get comments from the PDF form of an older document to the PDF form of a newer revision.

Acrobat Help content has useful entries for Import Comments.

In my humble opinion, every knowledge worker who touches PDF files should have a copy of Acrobat Professional (not just the free Reader). I may be biased — I worked for Adobe for many years, and I still hold their stock. But I believe that being able to do operations like importing and combining comments is hugely valuable for knowledge workers.