Cases and pouches.
I don't have dozens of guns, but do have the habit of my machining days of keeping precision or expensive tools and their accessories in their own specific cases.
So rifles get their own specific case. Each case has its mags assorted in the appropriate pockets if applicable. Non-mag pockets get the basic cleaning and maintenance supplies to take care of basic to middling issues at the range.
The mags that don't fit go into pouches. Stuff I can throw onto a shoulder and run out to the car if I have to get out of dodge. Something you think about when you have a hurricane season and you're 10 inches above water level between three ponds.
If they don't have pouches, of they're handgun mags, they go in an ammo can. Often loaded.
And all of them get numbered. Body, baseplate, and a non-contact spot in the follower.
Makes reassembly easier if I have to dry them out or something, and makes it easier to track down malfunctions.