A couple from Spec Ops: The Line.
The white phosphorus section, naturally, as you walk through the aftermath.
Then the ending when the whole story unravels and you realize the truth about the mission. You feel like you lose just about everything physically and mentally just to make it to the end and... there's no payoff. No feeling of success. I felt so betrayed by the game.
Pretty basic, but I don't normally figure out hacks/exploits on my own .
In Battletoads for NES, on the level where you ride the huge snakes shooting around the screen, there was a point where you could run and jump over a snake's head before it climbed too high and thus skip to the end of the level and avoid a few snakes.
I also believe there was a point in the swimming/pipe level where you could jump up and out, and skip a chunk of that level too.