I have a great bag from Ron at Mountain Laurel Designs. When I purchased a poncho from him, he also sent along a stake bag - he used a ripstop with spectra threads on the bottom of the stuff sack. Really, really tough material. It's the Dyneema X material he shows here.
For TI nail and shepherds hook stakes I also use some 1" tubular webbing and push the stakes into the webbing then the MLD stuff sack. I heat sealed the webbing on one end.