Well, it's time for me to put some input.
First off, I would like to say that them having no explaination in AoL or whatever doesn't necessarily mean much. Details and descriptions change and expand over time, so the best resource would be to use the most recent utilization of them as the "canon" content. We do this for game details such as background information such as the "legend" of Zelda, so we should conceivably do this for personal ponderings too, right?
Hypothetically, this should mean MM, but since MM is an alternate reality, they shouldn't be held as parallel and equal. Thus, this post will mainly be centered around my observations of the OoT Iron Knights.
I will be using this video as a reference point. The guy playing sucks, but it's a decent quality and shows everything I need it to.
[video=youtube;DTisSRx8EjE]http://www.youtube.com/watch?v=DTisSRx8EjE[/video]
First off, we have the possibility of them being possessed Gerudo.
There are three main reasons I doubt this possibility. Firstly, when an Iron Knuckle dies, it disappears/dissolves into blue flame. We see various magic/evil enemies do this (this is a graphical thing, so should only be related to this specific game), but we do not see human-esque creatures (ie; redeads), though we don't have any example of a Gerudo dying so we can't really say for sure.
Secondly, we have them in AoL. And although I know details have changed between the release of the two games, I do believe them to be, in essence, the same enemy, from the same origins. Thus, since we don't have Gerudo in AoL, unless the possessed souls can survive countless years until they are called upon again, they can't be Gerudo's (after all, considering Darknauts are essentially the same as Iron Knuckles but have different names and also different origins, we can assume Nintendo would have given them different names if they were meant to have different origins).
Finally, there are Iron Knuckles in the Gerudo Training Grounds. Now, no matter how strongly the Gerudo's believe in you, I cannot believe, at all, that they would posess their own warriors to stand guard in their training grounds to die by your hand. There's no way they would let you murder some of their best warriors and at the same time hand over their most prized possession.
So, as far as I'm concerned, the possibility of possessed Gerudo is out. Next, we have reanimated dead.
This can be supported by the video, in which, after the first layer of armor from the Iron Knuckle has been broken off, part of the forearm appears visable. It's possible it could be a leather under-armor, but it's eerily similar looking to the arms of a Redead. Take a close look at the video, then look at an OoT redead. They're the same forearms. This theory is also supported in MM since they appear prominently at the graveyard. However, MM isn't the same universe, so that shouldn't be qualified; not the same (similar enemy, same name, mayhaps) and doesn't count. Along the same lines, we can go back and look at the deaths again. An Iron Knuckle dies in blue flames. A Readead falls onto the ground and slowly dissolves. One could say that the armor is also enchanted, and that's what burns. And when the armor burns, the Redead (which would be roughly the equivalent of whatever reanimated is inside the armor, by this theory) would burn too. But the blue fire doesn't burn other stuff, as we clearly see many, many times throughout the game. This can be accredited to technical limitations, but it's would be immensely simple for Nintendo to have spawned a dead Redead onto the corpse of an Iron Knuckle; the blue flames would have hid the trick, and if they wanted a reanimated corpse to be the explaination I believe they would have done this very simple method of showing it.
Also, both of these are completely off-shot by the fight with Nabooru. When her armor falls off and dissolves, she is left behind. Thus, if there were bodies in any of the other Iron Knuckle, then we would have seen them when we defeated them, instead of the armor dissolving into the blue flames of nothingness.
Next, we have a ghost/dark entity possessing the armor itself.
The only defense I have for this is that the Gerudo, who we have no evidence are evil or necromancers or whatever themselves, have them controlled in their Gerudo Training Grounds. The remains of an Iron Knuckle do burn up like ghosts/dark entities we've seen (see Poe's, Phantom Ganon, etc.). So this possibility is still on the table, but unlikely. We have seen no evidence, including Kotake and Koume, of controlling dark entities or spirits.
The last possibility is that they are only animated armor themselves.
We have seen evidence that the Gerudo can animate inanimate objects VERY present in their temple in OoT. Even if the Gerudo didn't survive, histories of their magic could have outlived their race, which could explain how another power managed to do the same in AoL. It's also possible that the Gerudo didn't invent the magic of animating the armors, but they discovered it from another ancient race that came before them. This could also tie into the whole "Dark Tribe" thing. But besides from that, an animated inanimate object easily explains how they can be in both the Spirit Temple and Gerudo Training Grounds, and it explains how they can remain perfectly motionless indefinitely until disturbed, and it explains how they can easily have outlived the only peoples we know to have a connection to them.
So, in conclusion:
The most likely and almost certain conclusion is that the Iron Knuckles are in fact Enchanted or Animated armor, most likely of a superior quality. Better and/or more durable armors can account for the different difficulties between various Iron Knuckles, and the only body adds to IK-Nabooru's difficulty.
There's a slim, but possible, chance that Iron Knuckles are not being possessed by magics, but instead by spirits or entities. And given all the evidence we have, it's all but completely impossible that Iron Knuckles are possessed Gerudo (or any other tribe/faction), nor that they are undeads of any kind.