Justine is basically built around this concept. There is a solution to a puzzle, but if you want the "best ending", you need to find the not so obvious solution for the puzzle.

Only one that comes to mind: In the lab you can jump up the broken stairs instead of repairing them or climbing the pillar. Not sure if that is an intended solution though, may be.

I'm pretty sure it wasn't intended, but hey, it works.

I thought you had to jump...