For pistol mags I use 50 caliber ammo cans. I don't store loaded magazines. I keep all the mags for each individual gun in a large freezer bag and put the bags from the same caliber in the same can. Each can is labeled by the gun models contained with sharpie written on blue masking tape.
I have too many rifle magazines to do that with them, so I keep them in a rubbermaid container by type for some (AR, AK) and 20mm ammo cans for others (M14, FAL)