Oh, I almost forgot, I did manage to put together that list of games featured in the MIT Mystery Hunt that I mentioned earlier. Check it out, and add any games or references I missed.
There was a D&D puzzle, but that's probably not listed at Boardgame Geek. And there's the Boggle/Ricochet Robot game (http://www.mit.edu/~puzzle/03/www.acme-corp.com/teamGuest/3/3_7.html).
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And I couldn't think of any.
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