The particularly bad example that got me thinking about this is Deus Ex II: Invisible War. I was shocked when I looked at a walkthrough and saw what I'd been missing. My favorite example was in a coffee shop in a seemingly law-abiding area. The proprietor is standing behind the counter, chatting with a customer in front of the counter. Everything seems quite normal.
-- Under the circumstances, it NEVER would have occurred to me to just walk around the back of the counter and begin searching for stuff to take while the manager is standing there.
-- If I did, I CERTAINLY would have expected the manager to object.
-- Once behind the counter, I NEVER would have expected to find an ammo clip just lying next to the coffee maker!
-- And in ANY coffee shop where ammo clips were just lying around like that, I SURE would have expected to have been shot by the manager before I ever found the clip.
The entire scene was so utterly random, I suddenly realized that no rational decision-making processes had any value in the game. I kept playing, but instead of making decisions in character, I just became an automaton -- methodically searching everything everywhere, and exhausting every discussion tree with every NPC I met.