Magical Diary -- it has puzzles, although they're only a small part of the game. Ellen reminded me of Less Wrong fairly quickly; I later found out that TV Tropes lists her subplot as a shout-out to Harry Potter and the Methods of Rationality.
I played it a few months ago. It was quite fun... and, yes, there's one big shout-out to HPMoR (more specifically, to the Bayesian Conspiracy) in interactions with Ellen.
This is the monthly thread for posting media of various types that you've found that you enjoy. Post what you're reading, listening to, watching, and your opinion of it. Post recommendations to blogs. Post whatever media you feel like discussing! To see previous recommendations, check out the older threads.
Rules: