Some people don't consider this a puzzle, but I do since it's a fairly open play environment; getting the Clean Hands, Ghost, Shadow and Mostly Flesh/Steel Trophies/Achievements on Dishonored in 1 play through on Expert Mode.
Clean Hands: Complete the game w/o killing ANYONE (including key targets).
Ghost: Complete the game w/o alerting/killing anyone except key targets.
Shadow: Complete the game w/o alerting anyone.
Mostly Flesh and Steel: Complete game without enhancing blink or purchasing ANY supernatural abilities.