I keep mine underneath my bed. Half of the underside of the bed is taken up by a set of drawers that go with the bed, leaving half of the underside facing away from my bedroom door free. In 2011 I got the Legendary Edition of Halo: Reach, which comes with a box that holds the collector goodies, seen here. Well, for a while I was keeping shoes in the box, but eventually the box couldn't hold anymore pairs so I just kept them under my bed, covered with a guitar case.
That worked out for a year until one of my friends needed a place to stay and I offered him to stay with me (I still live with my parents). The only place we could fit him in was on the side of my bed away from my bedroom door, right next to my collection. Now, the wall beside my bed does this L shape outward from what would be a corner (there's a closet in the room next to mine). So what I did was take the shoes I had under the guitar case, put them under my bed back towards the headboard, and stored the shoes I love to fuck the most in the space between my bed and that L shaped wall.
Kinda risky having my friend sleep literally inches away from my shoe collection, but so far it's worked out. I have over 20 pairs. Three pairs I'm now keeping under my pillow (two pairs are flats and the other are the sneakers I made a thread about a while back). The only downside to this setup is that I can only fuck my shoes when my friend is out. Luckily he has a landscaping job that keeps him gone all day, and he has a girlfriend which he hangs out with most evenings.