Look at cold cathode, get some rounded cables, some wire tubing(to cover up wires), cut out some blowholes, add some of those new special fan grills(like the punisher, that one rocks), and add a cool case sticker.
You can always get an eq or some form of sensor that will output some leds or what not.
I saw a cool case in Maximum Pc a couple of months ago where the guy made a skull come out of his case and the eyes glowed red.
I'm in the modding phase right now too but I'm not sure how far I'm going to go. If I had seen this premade case before I ordered the case that I just sent away for, I would probably have bought that one(it is a black Chieftech? case with a green L shapped side window and a fan on the side with the Punisher fan grill). The case cost about $180 w/o psu.. but a very cool case.
Hehe I don't want to screw up my new case with a dremmel cause I would probably get the holes cut in it for a window or a new fan and figure out that it wouldn't fit or that's not the place that I wanted to have it anyway.