If you have a Dremel ($30-80 home depot) and a Nibbler ($10 Radio Shack) anything is possible. Most cases these days already come window'ed out but you can always add fans in trick places... on the other hand I have 21 fans in my Lian Li Server Tower with very minor modding and when I bought that case, I had to send it off to be custom laser cut for a plexi window.
On alot of cases that have the front panel that swings open, like the ThermalTakes, I usually just use a drill to drill out the front for better air intake. You can basically look at all the air inlets and just ask yourself, "how can I make this hole bigger/less restrictive".
One thing I have been wanting to do is to get a little DJ Fogger from guitar center and pipe in a mix of 60/40 smoke/air. Then at Petco, in the aquarium dept. they sell little laser beam kits for aquariums and shoot those lasers around in the smoke.... The only thing holding me back is Id have to build in a fixed piece of plexi inside the case and silicone it off so the Mobo is protected from the smoke... (its rather damp and can destroy circuitry).
Another fun thing that you cant really go wrong with is to take a crappy steel case and use a 4 1/2" disc grinder to take all the paint down to the steel and leave cool swirl marks/patterns in the case then shoot it down with Krylon Clear Coat.
Before bus fan controls were manufactured, it was pretty fun to make your own with about $15 in parts from Radio Shack... you can still find schematics on the internet on how to make them.
You can replace the Lights in your keyboard with LED's...
You can backlight your keyboard with a piece of cold cathode neon...
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