First a note about the case: You don't have to stick to the dimensions of the original one like others have done when re-homing these machines. The PSU is a straight ATX, which helps the slimming process. Check eBay for a 1U ATX server PSU or something.
A mod I have been thinking about, but have no real point in performing, is to swap a desktop optical drive for a notebook (slot load?) one. This should be simple enough, using only the small board that comes on the back of the optical drive in slot-load G3 imacs. I haven't quite worked out the pinouts to provide the power to it yet. Maybe you could try this out. You could probably put two drives in this way, and still take up less room than the old one. That might be handy in a media centre.
You can ditch the floppy drive unless you really need it too. So plenty of space to be saved, allowing a much sleeker case to be used.

You know you'll need Xpostfacto to run anything later than 10.2.8? They max out at 768MB RAM, which should help alot with OS X, but I'd recommend a CPU upgrade. These machines are not quick under X. G4 would be good for media usage. Especially if you want to burn DVDs or anything.