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Wow. I've got 2 shuttles, both SB series, and both are near silent when running. The ICE fan is temp controlled, and should only spin up to full speed when booting/restarting. Even under fairly high load, it never ran at full speed for me.
The first step... Kill your warranty by cutting out the fan grill on the back. Should drop temps by up to ten degrees celsius.
The next step is to find a different fan. The stock Sunon is a little bit on the noisy side. However for me the biggest sources of noise were my old hard disk, my 9800 pro and the power supply.
You should open the system up and see what you hear. The PSU you can replace with a SilentX 250 watt unit that is a fair bit less noisy. The hard disk you can replace as well. Fluid bearings are an important detail to watch for. Older Western Digitals are notorious for being loud.
I ended up sticking one of the Zalman heat pipe coolers on my 9800 pro. Not that great of a solution. Sure it's quiet, but it doesn't fit without modification if I want to be able to close the case. I'm still brainstorming a different solution...
If your system has a Northbridge that you think is noisy you can slow it down with speedfan.
We all have different ideas as to what constitutes quiet. My shuttle has always been quieter than my old full sized enthusiast rig. There were a few stock components that kept it from being as quiet as I wanted it... But for that I probably would need to get rid of all the moving parts. Which of course, isnt going to happen.
Now, after all of the modifications, it's down to a very unobtrusive hum.
Have you had any heat issues from your 9800pro? I'm pretty sure mine cooked not one, but two WD signature 180G drives. No problem running normal desktop apps, but around 1 hour of 3d-gaming, hard drive no workey.
That was the older SB51G, which definitely had ventillation problems. Haven't had a problem with the new system (20th aniversety edition), but i haven't gamed with that one yet. I'm thinking of adding a blowhole (if i can find room) to help draw cooler air into the case. I also need to do the ICE vent mod you were talking about.