So I've began modding a 120mm fan into the top of my Shuttle XPC. The hole is a bit rough as it was trickier and louder than I expected with a Dremel, but with a metal file it shouldn't take too long to sort out. Trying to find some U-channel rubber for the edging in the UK is a pain also! I also have a minimal black circular grill to allow maximum air flow and hopefully avoid anything falling into the fan.
The only down side to this mod is I lose a hard drive bay in the top of the shuttle. With three in there its not a massive loss, especially since I got a HP mini server for use as a NAS.
Next I have a 80mm side fan to do. That is going to make getting the case on and off a bit tricky though as its tight for space inside. I really need an in-take fan though as I have a lot of exhaust fans.