I like to keep my set up really clean, and clutter free.
I built my own cabinet and shelfs out of plywood and MDF. I'm not very experienced at making cabinets, but they're really simple, so they only took me a few hours each to make. The shelves on the cabinet unit can be slid out to vent the consoles, and to dust easily. I also run all of the wires into the wall behind the unit. I really hate seeing wires and cords. Here's what it looks like without anything in it:
My entertainment center cabinet and shelves are all just 28" high, so they aren't very cumbersome or overwhelming. I have sloped walls in my game room, so it was important to have a storage solution that took advantage of the all the limited space available.
I have all of the main consoles I play hooked up via 2 A/V selectors (and HDMI for the modern ones) which are tucked away behind the cabinet, and labeled. I usually just set any additional system I wish to play on top of the cabinet since there's free A/V port on the side of the television.
My space is limited as well. I have the whole attic to use as my game room, but the awkward walls limit the amount of usable space -- still, I managed to build storage that holds tons of games. I think that having low and shallow storage, rather than tall, deep bookshelf style shelves, helps a lot when you don't have very much room and want/need to keep it (relatively) minimal.