As a game designer it's always tough to judge how a particular puzzle will be received. (I must add that some puzzles in the game were partly / entirely designed by my co-dev, but you can blame me for most of them.) The final puzzle of the game in particular seems in retrospect to have been rather poorly conceived - it made (and still makes) perfect sense to me, but not to other people!
I think the puzzle I'm most proud of is the RoboMusic puzzle (encompassing all the samples you have to collect and how to make them sound right). It seems to have been quite popular with testers too. But what about you? Let me know what puzzles you liked (or didn't, I guess - I will try to take everything into account when designing the next Captain Disaster game!