For me that's the main problem of Apple headphones: they are utter crap in terms of sound quality.
Another problem I could see: you add weight to the chord which will make the headphones more likely to fall from the ear, that's a big deal if you do sports with it.
This is a cool idea but the price of rare-earth metals might be its undoing.
I haven't had issues with tangled headphones for years now...
Though Apple increased the stiffness of the stock earbud cords at some point, so using this method (IME) can cause the cords to spiral and twist in weird ways. The extra weight of some magnets might well hold down that problem. [2]
[2] puntacular
I had a pair of these:
http://www.google.co.uk/products/catalog?hl=en&safe=off&...
But the headband was too heavy to do any running or anything in :(
ps: it's pretty sweet how this problem belongs to Apple. If headphones are Apple's biggest product problem, it's because their headphones suck, not because the cords get tangled.
I'm not sure that I'd want to buy custom earbuds just for this particular feature. As jsherry suggested, this is something that (IMO) would be better licensed to name-brand headphone manufacturers.