I use USPS tyvek envelopes, plastic zip lock bags and or ripstop nylon stuff bags depending on the type of stakes.
Sometimes I just place them in a side pocket of my Go-lite Pinnacle pack. It's a stretch side, and holds them pretty good.
I'm a member of PETA!!!!
I keep mine in a small cuben bag....usually 6 mini groundhogs
"Go sell crazy somewhere else, we're all stocked up here"~Jack Nicholson/As Good As It Gets
I have a mesh bag that came with an old cook kit that holds all my lines, stakes, and associated kit. I store them in one of the side zip pockets on my Osprey Kestrel.
I solemnly swear that I am up to no good...
Currently I carry some dull and cheap stakes. So I have no problem sticking them in a Zip-Loc baggy with my cordage.