I've been thinking over perception and searching in gaming. The way I figure it, there are a few ways to go about it:
1. Negotiated: if there is a dagger +1 in the pile of moldering clothes, a character who rifles through them is going to find it. The DM might rule that a character who merely prods the pile of rags with his trusty 10' pole (to make sure that there's no monster hiding in there) might not find it. If there's a key in the third desk drawer, a character who says he's opening said drawer (or says he's searching the whole desk) finds it. End of story. I like this method because it rewards clever players, but it can also become tedious if the party stops to pull and prod every brick, book, and candle in whatever location they happen to be exploring. I've noticed that older games tend to at least partially treat perception like this, as do games that don't address the issue mechanically at all.
2. A flat probability. I'm not sure I've ever seen this outside certain rules in older versions of D&D: characters have a flat chance of finding a secret door, or a party has a certain chance of being surprised. (Which I think it a matter of perception) This tends to put characters on more or less equal footing,
3. Perception is a stat. Games I've seen that operate like this include all the old White Wolf games, "classic" Deadlands, In Nomine, Gamma World 4th edition, etc. I'm sure I could think of more if I tried. I have some misgivings with this method, because players get lazy and just ask if they can make checks with their perception stat. The DM can also get lazy, just setting up rooms and encounters to be contingent on someone passing a stat check.
4. Perception is a skill. This started showing up in the form of Thief skills (Detect Noise, Find/Remove Traps), and mutated horribly in the d20 days to be three separate skills. (My least favorite handling of perception in all of gamedom.) I have the same problems as above with #3, except this also forces the players to spend skill points/levels/whatever and makes them less capable at doing other things.
5. Perception is a roll you make with another stat. The new World of Darkness and it's various offshoots do this. I find that games often co-opt the system's equivalent of "intelligence" for this. I'm wary of game systems that overemphasize certain attributes by making them "too good."
Personally, I like negotiated perception the best, though I do see a need for a mechanical system to determine things such as surprise, and I can see the value of the old rules for finding secret doors. (Lest your session turn into "Okay, I tug every book on every bookshelf. I twist and pull all the torch sconces, I push ever brick in the floor.") I am also not a fan of adventures that hinge entirely on a successful search/perception/cognition roll to find a clue, key, or MacGuffin without which the party cannot progress further.
The more I think about it, the more I find that I dislike a mechanically standardized approach to perception. I think that it simplifies things, but ultimately takes away from the experience. However, there should be rules in place for things like ambush, or a character using "hide in shadows" while other creatures pass by.
I'll have to think on this further.