Since I'm a Tex Murphy fan, here are 2 puzzles that made me crazy.
Elijah Witt's Puzzle Box in Pandora Directive. It's a timed puzzle that'll drive you crazy.
The Alcatraz Bricks puzzle in Overseer. That one is like a blind person trying to put together a 100,000 piece jigsaw puzzle together.
Another strategy in Overseer that took me almost a month to complete is in the Gideon's Gallery. It's not really a puzzle....it's more strategy where you have to time yourself to get out of the Gallery before being zapped.