At some point, you need these puzzles to be involved. Yes, I've used these.
First one: Party descends spiral staircase. Due to the angles involved, you can't see more than 10 feet ahead unless you can see through solid stone. Everything around is stone, including the steps. Suddenly, whoever is leading finds one of the stairs is actually made of metal. This will naturally evoke suspicion. An easy Search check (say, DC 15) reveals that there is a crack between the wall and the stairs and there is a wire running from the metal stair into the wall. In fact you might even notice it without actively looking, say Spot DC 25 for the same information.
If you step on the step you get hit by a relatively weak spell that the inhabitants would be immune to or benefit from, but that would hinder any intruders. I used Inflict Critical Wounds. Adjust up or down depending on party level, but it's not really meant to be dangerous even if you handle it wrong. You could use some other spell if this is the base of some other group accordingly. Whatever.
Most will not step on the step. They will say Obvious Trap is Obvious, and disarm it.
Here's the kicker. This is the worst fucking thing you could possibly do. What you're supposed to do is trigger the trap. The reason for this is that triggering the trap disables a much worse trap a bit further down for a short time. If you skip the step, or disarm it, or whatever you have no choice but to trigger the second trap, as you can't get to it without first setting it off due to positioning. What is this horrible second trap you might ask? Why, it's the mighty Alarm spell, set to mental mode and tied to the BBEG, or some other such badass down there. That is nonsarcastic by the way. If you can't see how 'alert the BBEG right off, and you don't even know you fucked up' is a nasty trap then you clearly aren't making your BBEGs right.
The other reason it's so nasty? The inhabitants just walk down the stairs at a casual speed like normal people and never trigger it, though if one did trigger it by accident it would just put the base on standby mode without going ballistic. They identify their own, and continue their operation, possibly smacking the guy for pulling the proverbial fire alarm. End result is the BBEG doesn't lose more minions to his front door. Adventurers, who will naturally disarm the trap, and proceed at a max speed of 5 feet per 6 seconds due to Search taking a full round action? Oops. Suspicious behavior alert! If for some reason one was taken hostage, and made to lead the way he could also trigger the alarm in this way. He tells them to step over the trap. He's telling the truth - there is a trap there, which Search, Sense Motive, whatever will confirm. Then they get down to the heavily fortified front entrance and shot up by ranged attackers through arrow slits. The archers should actually be SAing with rays or something at mid and high levels to ensure relevance.
Fucking with expectations for the win.
Let me know if you want more.