I saw a picture on another forum where a guy used a automotive carb filter and housing on the side of his case with 3 80mm fans inside. He claimed it completely masked the noise and provided great air and filtered out all the dust. I thought this was a great idea as the filters are cheap and readily available at automotive supply stores. He got the filter holder parts at a salvage yard.
If you are designing from scratch, using parts from the automotive industry would be interesting.
Another thought would be ducting air through the case to provide flow across the drives where water cooling would not be appropriate. You could use plastic ducting pieces from the air conditioning or plumbing industries. Check on
www.mcmaster.com for some ideas. On that same website, search on "sound dampers". They have some commercial products that I have been using to stop vibration in my systems and to lower noise. You might be able to design some of the flat areas of the case out of these materials.