So I thought it might be a good idea to make a post showing the different internal workings so that anyone else looking online for that info in the future can find it here.

First off, here's the manufacture dates for the plastic casing for each of these:
Taiwan: 1994-05-09
Japan: 1994-06-?? (Circuit board says 1992)
Malaysia: 1993-01-??
Really I don't know if that means anything. The plastic for each was made pretty late in the console's lifecycle.
So now here's some pictures.
(warning: I picked probably the grossest controller for the Taiwan pictures. Sorry

First, the circuit boards for each:
Taiwan:

Japan:

Malaysia:

Some pretty significant differences here. Notably, the contact points are all different, and the chip for the Taiwan board is on the other side (There is practically nothing on the other side of the other boards). Also, the Taiwan cord has a bit of extra length to wrap around some plastic posts to prevent the cord from being yanked loose.
Next, here's the plastic casing with the rubber buttons in place.
Taiwan:

Japan:

Malaysia:

Taiwan and Japan are very similar. One thing I noticed different is that the posts in the Japan controller have a bit more plastic that pokes through the holes in the circuit board, so it fits in easier (though this doesn't matter once you get the back on). There's also an extra post on the Malaysian controller for the cord to wrap around (which is weird because the cord DOESN'T wrap around it...)
The obvious difference is that the D-Pad on the Malaysia controller is VERY different. It's shaped like a plus sign instead of a circle that the other controllers use. It also doesn't have any holes to fit over the posts to keep it in place, instead it has a lip around it so it fits over the plastic like a... plastic lid or something. After using this controller, it does seem slightly "snappier" than the others, but that might be all in my head.
Finally, here's the plastic below the buttons.
Taiwan:

Japan:

Malaysia:

Again, the only major difference is the plus-shaped DPad of the Malaysian controller. It's has a white plastic piece held on with a screw, which apparently also provides the rocking motion instead of the silver ball bearing in the rubber that the other Dpads use. I didn't think to try unscrewing it.
So there you have it. Can anyone explain why there are these differences, or even when these changes were made? The dates on the plastic molding don't seem to correspond to much. At first I thought the Japan and Malaysian controllers were released later than the early Taiwan ones, which made them rarer (I only had one of each, and probably 15 Taiwan ones), but the dates on the plastic contradict that. Is it just a case of different controllers made for different parts of the world, and two of them just happened to end up overseas near me?
I forgot to mention, but these are all white-label genny controllers, and they all look the same on the outside. I had a handful of red-label controllers, and they were all made in Taiwan.