In D&D (3.5 obviously
) there are certain concise mechanics for stunning someone, for immobilizing someone, for inflicting other kinds of detrimental conditions, and for non-lethal damage. There is NO rule for knocking people out cold by hitting them on the back of the head. To do that, you have to hit them until they drop from the non-lethal.
Now STILL many people will want to do "knock-out-ninja"-moves on people, or knock out a person with one blow. And people might say that "it's necessary for the story". It's NOT. Change the story. The world doesn't work that way in D&D! There are classes that can make sure you can in fact do this, with class abilities. A rogue with a sap for instance can sneak-attack with non-lethal damage and hence knock people out. A barbarian might power-attack with non-lethal damage. And yes, sometimes in order to knock someone out you may have to bludgeon him repeatedly until he drops. However, that's not a bad story, it's just different from what's in the movies. Hence, it's GOOD STORYTELLING to do this the way the rules work. If a D&D GM at some point were to say: "Uh, while you are standing around someone comes up behind you and knocks you out", I would politely ask him how much non-lethal damage I got, or which condition he imposed on my character. And if I later meet that NPC and he says it's, let's say, a fighter, then I would ask what ability he used to inflict that much non-lethal in one hit. If he has an answer, fine. If not, then that's something that just won't fly, and I'll flat-out tell him that what he did doesn't work, and he shouldn't do it again.

Now STILL many people will want to do "knock-out-ninja"-moves on people, or knock out a person with one blow. And people might say that "it's necessary for the story". It's NOT. Change the story. The world doesn't work that way in D&D! There are classes that can make sure you can in fact do this, with class abilities. A rogue with a sap for instance can sneak-attack with non-lethal damage and hence knock people out. A barbarian might power-attack with non-lethal damage. And yes, sometimes in order to knock someone out you may have to bludgeon him repeatedly until he drops. However, that's not a bad story, it's just different from what's in the movies. Hence, it's GOOD STORYTELLING to do this the way the rules work. If a D&D GM at some point were to say: "Uh, while you are standing around someone comes up behind you and knocks you out", I would politely ask him how much non-lethal damage I got, or which condition he imposed on my character. And if I later meet that NPC and he says it's, let's say, a fighter, then I would ask what ability he used to inflict that much non-lethal in one hit. If he has an answer, fine. If not, then that's something that just won't fly, and I'll flat-out tell him that what he did doesn't work, and he shouldn't do it again.
So your problem is that you want to be a rules lawyer and you can't if a GM doesn't follow your rules? Do you ask for the character sheets of every NPC you encountered throughout the entire campaign and look at the average and standard deviation of their stats to make sure that the DM really did use the 3d6 method that the rules say a standard NPC has? Or that he at least used the nothing more than the elite stat block? Do you also expect a full accounting of the economics of the dark tower and where the evil warlord got the expertise and money to build 3 fireball traps when the ruins of the town only contained 20 goblins, so it should only be a small village and gp cost is too high for a small village to provide those traps? Do you want him to justify how the miners managed to make it through the rock with picks that cannot deal enough damage to overcome the rock's hardness? and then let the group vote on whether or not his explanation and house rule for that was plausible enough? and then make available to you a special 3d6 damage rock pick, because you can't accept that rules are be necessity abstractions?
I think you're being a bit ridiculous. Yeah, as a player it is wrong if a GM just arbitrarily said something I want to do does not work and the rules should usually be followed, but if a GM wants to say that a monster or villain does 5d6 nonlethal damage in an attack or that the Threshold to hack an ultra-high security node is 7, without having built entirely through the feat tree or scoured through Unwired to get the exact way that it works, that's fine. He or she is creating challenges and a good GM will create them at an appropriate level where they are difficult without being impossible. Obviously, the GM should not just say, "You fail, you lose, because I said so." and change things randomly, but I don't think anyone is actually expecting that from a halfway decent GM. I am fine with my GM saying, these guys do X damage, because that's how much they need to do for this to be exciting, even if the books says that they only carry X weapon which does not do that much damage.
I just quit a campaign that fit perfectly with your "ideal" way to play. I quit, because it was horrible. The GM laid out a world at the beginning, following all of the D&D 3.5 rules, and we all agreed on types of characters, races, the equipment that would be available. Then he laid out a 50 by 50 miles stretch of desert we were operating within and filled it with NPC's and PC's, he actually built entirely within the rules, buildings, monsters, treasures, etc. We spent hours rolling navigation checks, worrying about dehydration, moving through the desert, rolling for the chance of random encounters on the set schedule, talking to people that were little more than scenery, and never got anywhere or did anything fun. If the GM had been willing to just railroad us a little towards what was exciting within this desert world or towards a story, it would have probably been a great sandbox game. But he wouldn't because "He did not want to break the rules, because that would be cheating." There are times where the game is more important than the abstractions of a world that the rules represent and I prefer a GM that is willing to recognize that and act on it.