You could very well put Windows 3.x on there. The problem, of course, is that the DS has a different hardware setup, and would have to have a customized version of the OS. Also, as was mentioned above, the source code really isn't available. If someone really wanted to, they could program something similar.
I've seen some multi-threading examples, and they ran slow, but there's a lot to be said about tricks-of-the-trade and coding things to run with incredible efficiency. Simply put, Microsoft probably makes a more efficient system than most homebrewers can, even if Microsoft is inherently inefficient.
As was also pointed out: What would be the use? To run a game or other program, the entire OS would have to be unloaded in order to boot the game. If you wanted to get back to the OS, the best you could do is wrap some additional code to the ROM, like most flashcarts do, to reload the OS when you press a button combination. At that point, you might as well just use your flashcart's filebrowser.
If we ended up creating a very slim OS, and then standardized a method of creating small DS applications, we could potentially plug them in and run them directly on the OS. These would be low-feature programs, though, and it wouldn't be likely that we could run more than one or maybe two at a time.
You know what I'd like to see? Swap-files on the MicroSD. Expansion RAM is probably a great deal faster, but you could store a gig or two on your flash card, unlike on your RAM.