Most of the ones I've seen use the original controller's PCB, then wire a converter circuit into the controller's output pads and the USB cable comes out from there, but it's probably different for each one. If you want to know about a specific one, you'll have to provide more details.
I highly doubt there is more than one company making these as it's a fairly specialty item. Furthermore, they all seem to be sold by the same companies that re-brand a bunch of other imported clone hardware (Hyperkin, Retrolink, Tomee, etc.)
Since people seem to favor Retrolink (in spite of it probably being the exact same controller everyone else sells), I'll use them for the sake of discussion: http://www.amazon.com/RetroLink-NES-Cla ... 295&sr=8-4