Many of the indirect segments of Deus Ex: Human Revolution's area designs. There were quite a few sneaky areas in the first real "level" of the game that I just completely missed the first time I played the game because I was so used to the most direct path being the only way to proceed. And the first time I played, I snuck into the back of the police station and had to basically take out the entire building, whereas the second time I just talked my way through the front door.
Such a great game.
There are almost certainly many more, but I've played so many games that I can hardly keep straight all of the ones I played last year alone, say nothing about over my entire life.
Oh, wait, I've got another one.
In Sonic's first stage of Sonic Adventure 2: Battle (at least the HD re-release, I can't easily verify the original Gamecube or Dreamcast versions), "City Escape", there's a spot shortly before the second massive downhill road (I think) where you go up a flight of stairs and hit bouncy springs which lead to another set of stairs between small outcroppings where enemies fly down as you run past them. If you spin dash on the first flight of stairs, Sonic will overshoot the bouncy springs and transition into an actual wallrun up to the second flight of stairs. It's the only spot in the game where I've seen the player be able to make Sonic wallrun without the level architecture automatically pushing you into it beforehand.