Having to keep my collection in my bedroom means space is always at a premium, but there is some method to the madness. My entertainment center consists of a large, 2 sided Besta shelf from Ikea, and a heavily-modified Journalist unit (also from Ikea, long since discontinued.) Against one side of the besta unit is a very small media shelf (something like 15" wide by 3 feet tall). This is the portable games area- DS titles of all kinds are on the mini shelf, plus Game Gear games & Vita games split between the top shelf & the top of the unit. Above that is a set of hanging baskets from Daiso holding PSP games. On the top corner of the Besta unit, as well as one shelf, are cartridge-based and boxed portable games, along with a bunch of extra Game boys and accessories. The upper half of the besta unit is pre-crash systems and games, as well as my Sega Saturn games. Crossing over to the Journalist cabinet, you have the rest of my CD-based games. This is all in a general inverted L shape game-wise... for the most part, going left to upper right, then down, the games go from older to newer. My post-crash consoles are on the Journalist shelving, all hooked up & ready to play.
Across the room at the foot of my bed is post-crash cartridges. There's a wire media rack holding boxed carts, and a 3-tier rolling drawer unit with loose carts & the cables/controllers for the pre-crash systems. The rolling drawer doubles as an extra shelf to set up the pre-crash systems on when I want to play one. All my other controllers are in a modular drawer unit in the closet. Large specialty controllers are in the front of the cabinet above the closet. Finally, portable systems are stored under the table my stereo is on.
To maximize space, rather than store my games in library rows, most of my collection is stored in front-to-back rows in drawers and decorative boxes. This lets me use deeper shelving to hold more titles in the same amount of wall space while keeping things in relative order. Games are sorted by console, then alphabetized with imports mixed in appropriately- I own very few imports, so it makes more sense to just keep them in place right now.