The One, The Many
As with many who otherwise enjoyed The Matrix, I found the "humans as power source" excuse somewhat disappointing. I have heard that in the graphic novelization (which I have not read), an alternate explanation is provided: humans are connected to the Matrix because the machines use human brains to perform vast computations. This has some compelling implications. For one, if some percentage of the capacity of your brain is being stolen from you, the human mind may have limits far beyond what are normally experienced. For another, if the Matrix is computed within human brains, the simulation may not have to be generated as direct sensory signals and piped in from the outside. Instead, the ideas of objects and events can be provided as suggestions, and the enslaved mind can be made to fill in detail at any level, as in dreams or True Names. Most importantly for my purposes, if the human brain is being used to compute the Matrix itself, then it gives a natural explanation for the power of The One.
Imagine that you notice a train of thought carrying on in your mind, seemingly out of your control, like perpetual motion just out of your field of vision. It doesn't make any sense, doesn't form words or images, but it keeps distracting you as you go about your work, do your taxes, and help your landlady carry out her garbage. Eventually you begin to notice patterns, almost premonitions. You cringe in recollection just before a glass breaks in another room. You recognize the feeling of an unexpected guest moments before he rings the doorbell. All the stuff of coincidence, or superstition. But then one day you see it again, the harbinger of smashed china, and you deny it. You master the mental loop that was driving you to distraction, and you find peace. Rather than a smash, there is a shouted obscenity from the other room. You investigate and find your coworker standing staring at the coffee mug he had knocked off his desk. It is now hanging in space several inches from the floor. As the shock hits you, the mug hits the ground and shatters.
If you can excuse my attempt at prose, the fascinating idea here is that certain tasks of the world simulation are being delegated to the audience of the simulation. Normally the system is set up so that the tasks are carried out subconsciously, but perhaps there are flaws and certain people at certain times begin to notice. The brain being the powerful pattern recognition engine it is, it may manage to "decode the Matrix", at least on some intuitive level. Furthermore, some small set of these people may be able to manipulate these alien thoughts to reshape the world as they see fit. It doesn't perfectly fit with the cinematic fiction, but it provides some interesting possibilities for games about programming.
As an example, any kind of game with a physics system might occasionally interrupt play to ask you to solve a simple math problem. If you can recognize the numbers, say perhaps they are associated with the movement of an enemy you cannot pass, then you might be able to fudge the result to move the enemy in a physically impossible way. You may need to budget such abuses in order to avoid the system noticing and cracking down on you. From the perspective of programming, you may be required to simulate some instructions in your head or on paper, and doing this subtly wrong may likewise give you some advantage. It may be possible, and necessary, to examine the surrounding code (which is executed by other enslaved minds) to see what you can cause to happen indirectly. You may eventually get the opportunity to create new code and pass it on to others. As in the example above, even simply not executing some code may have powerful effects.
We see a similar thought in Neal Stephenson's Diamond Age, which describes a vast organic computer formed out of the minds and bodies of a society called The Drummers. The members are under the influence of nanites (nano-scale robots) that cause them to live in a continuous dream state, with frequent orgies for information exchange. This system is apparently used perform the massive computations needed to crack cryptographic protocols. The character John Hackworth unknowingly enters one of these colonies at the behest of the mysterious Doctor X, and something interesting happens when his engineering expertise is added to the mix. Normally someone who joins the colony loses any individuality and becomes just another part of the larger system. Hackworth, on the other hand, is able to take it over from within, and he uses it to work on an extremely complicated machine, though when he emerges he is not consciously aware that he has done so. A spectacularly different outcome of exploiting hive intelligence occurs in Bruce Sterling's Swarm. What other possibilities might we find in the concept of overcoming our role as just another brick in the wall?