I was on the team that won the shredder challenge. I talked to one of the UCSD people afterwards and he practically convinced me that my team did it. After a while I realized that it was so damn easy to sabotage their effort that I didn't really care if my team did it because that's what happens when you invite the whole internet to your party. Now I guess they managed to clear us of that. :) Unfortunately, when this Adam guy wrecked their program, he wrote them a letter which simultaneously implied that he was our team and the group "Anonymous" at the same time. Some people at DARPA seemed to believe that claim (even though I used my real name to sign up) and so DARPA was very hesitant to announce that we had won the competition. It was a fun competition though.
I worked with Keith at the time. Wasn't it true that you guys figured out that the yellow paper had a regular blue dot pattern watermark, and that you were able to use them to help solve that one? If I recall correctly, DARPA didn't know about that.
Yes, one of the keys to reconstructing the harder puzzles was that we found a yellow dot pattern on the paper. At the time, I was reading HN and I saw a headline that said something about the government tracking photocopies using little yellow dots. DARPA had photocopied all the docs before shredding them, so they all had a very high-res repeating dot pattern on them. We made our program snap the pieces to the dot pattern. With that in place, the puzzles came together relatively quickly. Some people at DARPA knew about the concept of little yellow dots, but didn't think much of it. I don't blame them. The shredded pieces were so small that it would be hard to imagine any secret pattern helping with the reconstruction. But I guess it helped enough. :)