a little bit more spec info would have been useful, however here are some general tips:
PSU fans: whiney and small, will be very hard to change this. will have to live with that noise unless you want to risk your life opening a PSU. NOT RECOMMENDED.
CPU/chassis: replace with 80/92mm fan (whichever size it is in the shuttle, depending on chassis) which is listed as fairly quiet but can still push some air if needed. this is the main cooling fan of the system, so a slow quiet fan can cause heating issues.
Graphics card: again depends on chassis (P/G), make sure the fan is always clean, try to remove dust. oil if needed and spin it for a while out of the system to ensure oil isn't spread throughout your system. a rattly GPU fan is often the cause of most of the noise in a SFF system as aftermarket coolers cannot often be used.
as stated, it depends entirely on what shuttle you have and what kit is inside it before we can offer specific advice.