using rubber washers between fans and the case should dampen a lot of sound. in my experience probably about 60-70% of sound is caused by the case vibrating so using rubber washers and basically padding anywhere where the case can vibrate against something or vice versa. using fan controllers or voltage modding fans may help to reduce overall sound. probably the best thing to do is to make your cooling more efficient to reduce the need for fans.
p.s. hdd's and cd-roms cause quite alot of vibration too and the idea of silencing them is to "decouple" them from the case once again with the use of something like a rubber washer. noisy hdd mechanisms could be silenced by using enclosed hdd coolers such as those Vantec make as for cd-rom's though i'm not sure.