Nice system!
I had a nice fancy case before too. I even had a clear acrylic one with blue CFLs at one point. Now days I just have a cheap rackmount case and the system is in the basement. I still need to run some cat6 for the power/reset buttons so I can toggle those from upstairs. I might get fancy and actually build a small panel with LEDs to show other info too and just multiplex it over a few wires using an atmel chip or something.
The cabling is a huge mess though, all the slack is shoved under the desk so the server rack can be kept cleaner. I eventually want to build a desk with a proper raised cable tray to snake the slack into. A "service loop" so to speak.
I have two systems though, my daily driver which runs Linux and then a Windows one for games, so that was one of the things that prompted me to move them downstairs, it was just too noisy and too dusty to have them in the office and took up lot of room.