Well, I store most of my various games and game related things in and on my computer desk. The games, game guides, and Zelda Soundtracks I have alongside the Hyrule Historia all take up the large alcove on it, inside the one cupboard are tins full of the rare Pokémon cards I collected in my younger years among other things, and then on top I have the large cardboard ? Box I got from Club Nintendo in 2010 and inside of it are all the various Mario figures I've collected.
Next to my bed and up on the wall I have two cases though, on is an older DS Mario case that I have my DSi in, and also my Sonic Screwdriver is placed in the one pouch alongside a larger 3DS stylus that I use with my Wii U gamepad from time to time. The other case s a Poké Ball one for my 3DS XL, in it I have all my Pokémon games, a Pokémon X and Y cleaning cloth, some extra larger 3DS styli, and Action Replay.
Then there's the one backpack I have hanging on the door to my closet, in it I have various weapons such as my machete, my battle axe is leaning up against the computer desk alongside a few other things though, and my grass cutter sword is right next to my bed where I can get to it easily. In the closet itself there's not much, I have my clothes in there and a box containing various things, such as binders full of my old drawings and collectibles that I threw in there so as to not make a mess of the place. Anything that wouldn't go in the box is just lying around it on the same shelf, there's just stuff like a lantern and other 3DS cases that I have.
Oh, and of course my Wii U itself it just stored in the space below the T.V stand I have, however the charger for it and everything is in front of the large ? Box on my computer desk.