I don't really remember his gym so well in OR/AS but the fracturing ice puzzle in Emerald (and I believe Ruby/Sapphire if I remember correctly) was great. It forced you to plan your route out in advance but if you thought it through for a minute it wasn't hard to find the right path.
The holes in the floor in the interior of Mt. Pyre and the Sky Tower too. I think there was a silly and untrue rumour back then that if you fell down even one of the holes, your save would be deleted and you'd have to start a new game all over again.