Mini-iTX stuff can be silent (EPIA500/2688 or EPIA-M6000 & 2699) - but can be a little underpowered for some tasks.
If you need more power then currently, the SHuttle XPC's are the quietest SFF PC's around. They are certainly quieter than your average PC - but not silent & you'll never make one silent. You can make them whisper quiet - see this thread
for more info.
You'd best decide what exactly you want to do with your machines & this should either steer you to a mini-iTX or Shuttel solution....
Hope this helps.