I am a little confused as to how to run perception checks for secret doors. Can a player notice a secret door by walking past it....IE huh thats an odd crack, what do we have here? I understand that it is a move action to actively search, but what about when you first walk into the room. The core rule book states as follows, but what is an "observable stimulus"?
Action: Most Perception checks are reactive, made in response to observable stimulus. Intentionally searching for stimulus is a move action.
It probably has to be reasonably obvious without spending the move action, like a good sized perfectly vertical crack at the door seam. Also I'd rule that there can't be anything distracting them like a bad guys.
Have you watched The Temple of Doom? There is a scene there where Indiana finds a secret door using candles or flowers (I don't remember which) to see a slight breeze coming from a secret room.
Discoloration of the door or surrounding area is another thing. Scraped floor, dust displacement, insects moving through small spaces, water or other fluid flowing where it shouldn't, a strange and muffled sound coming from the other side, etc.
This is great question, and one that I think can really affect a game depending on how you've decided to run it. I'll just give you a few examples of potential playstyles, and hopefully they'll help you to formulate your own way to run this in game.
First way to run it is, quite possibly, the slowest and most time consuming (especially for a dungeon crawl type of quest). That is to have the entire party roll a perception check whenever they enter a new visual area. Just turned a corner in a dungeon? Roll perception everybody. Entered a new room? Roll perception. Descending a stairway? Roll perception. You get the idea. This is, mechanically anyway, the most consistent and PC favorable way to run it. Consistent because it doesn't give anything away, and the PCs are the ones rolling the checks, which according to RAW is how it should be.
Which leads me to the second way to run it. That is to have the PCs roll perception when they enter any area where there is something that you know they might want to perceive (secret doors, hidden caches, conversation happening in the next room, etc). Problem with this? You just gave away that there's something they want to perceive, and just about any party worth its salt is going to then (outside of combat) take 20, and find whatever it is you were checking to see if they saw in a reactive way. So now the idea of reactive perception becomes almost entirely moot. This is a much faster way to run it, but it severely hampers the realism of perception from a mechanical point of view.
Here's a third way, and honestly the way I run it most of the time, as long as the PCs are agreeable. Find the person in the party with highest perception bonus. If there are PCs that are better at one kind of perception than another (i.e. trapspotters, scent users etc.) make a note of their type of perception and the bonus. Then, and again here, you need to make sure the PCs agree to this before the campaign starts. Assume that that PC "takes ten" (this assumes again that they are not in immediate danger) every time they enter a new stimulus area. What this means is that you the GM have a static number against which to check DCs for hidden items. Ranger has an 11 perception bonus? Every time they enter a new stimulus area they've rolled a 21. The table under perception says the "average secret door" is a DC 20. So when they enter the room you can just say something like: "You notice a draft from the brickwork... or whatever." This means that they've made that initial reactive perception check, and you've provided the info, and if they want to then (when not in danger) take 20, it's not because you gave something away it's because their character noticed the stimulus in a reactive way, just as they should.
There is one other way that I've run things in the past. This one also needs to be agreed upon by the entire party before a campaign starts. That is to tell the PCs that you will be rolling all perception checks, no exceptions, from start to finish. They can tell you at any time they want to use that move action and actively search, but you will be rolling. I would not recommend this one unless you are a GM that uses a laptop. Reason? I've had savvy PCs catch on to the fact that when I roll dice as they enter new areas I'm rolling perception checks, and they'll then ask to make a perception check and take 20. With a laptop you can create a handy "PC perception check Excel worksheet" that will roll d20s and add the perception bonuses for the entire party at the click of a button. That way you don't have to roll perception checks in every new area, you can just roll them in those rooms where there's something that needs perceiving. (It takes a very savvy group indeed to realize that one little button click is a hint that they should be actively looking for stimulus; especially if you use the laptop for a lot, which I do.) If you want an example of a spreadsheet like that let me know, and I'll upload one to google docs.
Hope this helps!
The White's very right about just rolling for no reason to throw off the party's "perception scanner." It is a very easy solution. I have done that in the past, the only reason I don't like that is that it puts a LOT of extra rolls into a session (at least it has with my PCs). Me rolling d20s for no reason, then, many times, they say they want to actively search, then they're rolling d20s, all with nothing immediately observable. Sometimes, if they rolled low enough, they'll roll again until they get a high number, at which point I'm forced to say "you don't see anything of interest." It does, definitely, create an environment of mystery, because they never know what exactly you're rolling for. I just like to streamline things a bit, and the fewer rolls we all have to make the better. That could be (read is) a by product of the fact that our gaming sessions are always short, and I like to pack in as much as possible.