Will be finishing up a review of the Shuttle ST61G4 soon. And there is a review of the Shuttle zen on the main site -- it's quiet, acceptable to me even in stock form.
1) There are several threads by folks who have successfully modded & silenced Shuttle boxes. Search & review.
2) The grill for the ICE fan exhaust is too restrictive & should be removed.
3) The 80mm HS fan can be replaced with a quieter one -- and mounted on the outside. This will reduce the noise, counterintuitive tho it may sound. (Has to do with turbulence/resonance issues.) Leave the shroud, I think.
4) Try removing any chipset HS fan -- or running it at reduced voltage anyway,
5) Their SilentX PSU is quieter than the stock one, for sure; no easy way to mod the wee PSUs. A major job.
6) Some versions have a row of tiny intake holes at the front on the bottom panel. These can be enlarged for better airflow.
7) Do whatever you can to damp the panel. Just placing a heavy vase with a felt bottom on the top of the box can help. The aluminum panels always resonant more than steel.
Go for the coolest CPU you feel comfortable with, and undervolt it. (Doable on many if not all Shuttles.) They're tiny boxes, and the airflow is nowhere as good as a good midtower.