I run FDE pmags in 5.56, and barrett mags for the 6.8. I have two HK mags left for 5.56 that are pretty well beat up (50% finish remaining at best) but I only use them for plinking at the range, no hard use.
I too had been debating what to do with my mags...I've got some PRI mags that are easy enough to tell apart, but I have C-Prod 25rd mags that are SS and look very similar to my 5.56 SS C-Prod mags. I just got a small stensil at hobby lobby and used flat white spray paint....here's a pic.
My 5.56 are all old aluminum GI surplus. My 6.8 are all shiny black, new and heavier.
Weight alone is enough to tell them apart. And I tend to segregate the stuff, anyway. All these ideas are good, though