https://imgur.com/Gfv8nmZ
Couldn't figure out how to post a photo, here's my shelf.
Ok, I see some familiar problems here...
1- Stop double-stacking! I know you're just filling in the space, but having a horizontal row on top of a vertical row never looks good. Either put everything horizontal (which will make pulling games out damn hard), or leave the gap. Which runs into...
2- Get more shelves! You absolutely have room to add more shelves into that space for better optimization. It'll be tricky, becuase it looks like you're using a small closet as your shelving & those aren't really designed for add-ins. If you're not willing or able to bust out the toolbox, look into monitor risers and dish holders- stuff like
this, or
this, or
this... there's a TON of these, in all different styles and sizes. Measure your space & shop around.
3- Sort your things! I see PC games, then PS1, then consoles, then PS3, then books, then DS, with controllers scattered throughout... these are all different sizes! It looks weird!
4- Boxes! You've got a lot of loose controllers and cart-only games hanging out, and those all piled up tend to always look cluttered. Get a nice decorative box (or boxes) to put them in. It'll keep things handy & hide the mess.
If I could magically transport to your space & set that up my way... I'd put books on the top shelf (Since those are always different sizes, and the top shelf is the hardest to modify). I'd consider upgrading your manga to omnibus editions (to save space) and getting rid of vol. 1s for series you don't intend to collect more of.I'd get a box to hold your miscellaneous media (like the diskettes and the VHS) so it's not stacked up. I'd bring up the handheld stuff to the next shelf & add a shelf or riser into it so the DS cases could all sit vertically. I'd get a small box for the loose games & keep the handhelds up there too. The next shelves would be ALL games, starting with PC & getting a CD wallet for those loose discs so you can get rid of that mostly empty giant disc spindle. Then set up console stuff moving oldest to newest. I might put the PS1 games in a CD storage box to keep them in a front-to-back row instead of a side-to-side one. Saves space. Then, at the bottom, I'd put all the consoles, and a box or two holding all the cables & controllers. I'd add shelving wherever made the most sense.
Alternatively, I'd put drops on all the shelves under the books/handhelds to hold the consoles, then put the games underneath. I'd still probably put the controllers & cables into a box at the bottom, unless there was room on the drop shelves.
It'll take some planning, but that'll tidy up fairly well with a little effort.