Typical gun safe interiors are poorly designed for handgun storage. There are usually just a few shelves as if the average gun owner has 20 rifles and shotguns, but only five or six handguns. You can usually add more shelves, but they have to be spaced far enough apart to be able to reach to the back and there's a lot of wasted space.
I've tried most of the things suggested in this thread - socks, gun rugs, in the box, racks, etc. Most of them have the drawback of not being able to see your guns, and that's one of the pleasures of ownership. Most of these schemes also make it difficult to locate and get to any given individual gun.
So, I decided to take matters into my own hands and build a safe interior just for handgun storage. (I now have a separate safe for my long guns, and more handgun storage in the future - if I need it!) I gutted my old safe and built an interior with drawers on heavy duty, full-extension ball bearing slides, and actually
just got finished with it this evening. I haven't lined the drawers or arranged my guns in it yet, but I did fill up one drawer just to take a picture. There is essentially zero space between the drawer fronts and the inside of the safe door when it's closed, nor any space behind the drawers. I had to spend a couple of hours tweaking the drawer slides to get the door to shut without forcing it.
Each drawer's interior dimensions are 18" deep by 19-3/8" wide, and about two inches tall. One drawback is that the drawers can't be any wider than the door opening (or course!). Gun safes are always made with a wide lip on each side so there's a fair amount of wasted volume on each side of the stack. It's a tradeoff.
Now I'll actually be able to see what I've got, and get to them easily when I want to go shooting. I'll number the drawers and stick an index on the inside of the safe door. All I have to figure out now is how to categorize them....