Cryptic Crossword: Amateur Crypto and Reverse Engineering
muppetlabs.com
muppetlabs.com
(At the time I was using a modified version of the "xword" program in Debian's repo, which didn't detect whether the file was scrambled. In other words, it treated every letter as wrong because it didn't match the enciphered grid. I ended up hacking in some code to detect these files and disable the check/reveal features when playing them.)
EDIT: To be precise, there were still a few other crossword publishers using the scrambling feature. None as important as the New York Times, though, of course.
It's such a good read that this is almost beside the point... but, as it happens, I worked on and reverse-engineered this same "encryption" scheme (I hesitate to use the word) for an iOS app that never shipped. I just dumped the code (which seems to have been written in late 2008) up on github... it's old, and messy, but hey, maybe it's fun for someone:
"My response was: maybe. Hard to say, but I'm willing to try. Privately, though, my reaction was THIS IS MY DREAM PROJECT AND THERE IS NO WAY I'M NOT SPENDING ALL AVAILABLE FREE TIME ON THIS."
While the second part of that is an interesting observation, the first part is simply false. It basically comes down to prior probabilities and conjunctions. Every bit of new information implied by a hypothesis is another "and". It is a simple fact that P(X) ≥ P(X and Y), so the more conjunctions your hypothesis implies (the more complex it is) the lower its prior probability.