Santa Fe Stoneworks and the Yellowhorse family are places where that kind of work is done. Santa Fe will do custom jobs for you, Yellowhorse are usually limited editions of production knives.
Santa Fe Stoneworks is probably who did the Spyderco knives you've seen. I have a Kopa where they did the gold-lip pearl. There are also lots of Kershaws, esp. Leeks and Chives, as well as some old-stock Camillus and Boker Magnum designs.
Just do a search for SFS on that auction site, and you'll see the variety available.