Of course, you can always install a dashboard like Avalaunch and change the voltage on the fan to slow it down and reduce the noise a bit, although i'm not sure what happens when you boot into XBMC or whatever. I don't bother because my 250Gb HD is probably louder, and my sound system even more so :-)

Of course, you could just replace the fan if you are that bothered - if I remember correctly they are just standard 80mm PC fans. Maybe something from Quiet PC or similar?