You can add insulation to the inside walls to absorb sound and you can isolate vibration from fans and harddrives. Also I think if you build a box that you put over your fans with insulation inside so the sound can't get right out, it will lower air flow slightly but make it much quieter. This is a small diagram.
There are kits for insulation type noise dampening, but not for muffler type boxes as far as I know, HERE is the article I originally saw about the mufflers. His are ugly and I think they would be better if he had put a baffle in like I suggested.