How you store your maps probably depends mostly on what you use them for.

My canoeing, topo, and geological maps exist mainly so I can take them out into the field and use them there. So all of my paper maps are folded and kept in manila folders and archive boxes until I need them.

Nowadays, I store my canoe maps electronically. I use Photoshop format, because I'm willing to sacrifice automatic mapping features (eg updating PCD data) for cosmetics. (Also because I already have a copy of Photo$$$hop).

Once my route is finalized, I print out 1:50000 custom maps of the relevant sections onto waterproof paper. (Somewhere there is an existing QJ thread on WP paper and custom mapping, started by DentonDoc IIRC). When it's time to go, the relevant maps (normal paper or WP paper) go into a ziplock bag for protection.

Folded or 8.5x11 two-sided custom maps aren't especially convenient if you want to spread them out at home for planning. If this is the main use for your maps, map cases, hangers (as shown), or rolled-up makes a lot more sense.

Most of my working career was spent in the oilpatch, and we used maps for everything. Only a few were kept in map hangers, because our maps were always getting updated, and you always needed to pull out one or two specific ones to take to some meeting or other. So most maps were kept rolled, and everyone had a cheap wire-frame holder for rolled maps in the corner of their offfice.

Rolled maps have one disadvantage: they tend to curl back up when you try to spread them out flat. So every office and conference room kept a supply of "shot bags", little (1"x2"x3") leather bags filled with lead shot, used solely to weight down curling-up map corners. That was much easier than trying to use coffee cups, staplers, scotchtape holders, or whatever else you could find. For anyone who keeps their canoe maps rolled up, I'm sure you can find shot bags cheap at any drafting supply store, maybe Staples carries them too.