with my mdd, i replaced all the fans and it made it so quiet, it's comparable to a mac pro.
the psu fans i used 2 noctua 60mm fans. the fan connectors i had to switch a couple of pins around and they plugged into the psu pcb just fine.
as for the main 120mm fan, i used a quiet but powerful coolermaster fan that pushed 70+ cfm with a 19db rating.
i also attached 2 slim 60mm noctuas behind the cpu heatsink and they were connected together with a splitter and resistor and then the wires routed to plug into a molex plug.
as for the cd drive exhaust fan, i left that one alone as it worked fine and was quiet.
i also had a couple of noctua 60mm fans for the bottom inlet of the mac. those were connected together with a resister and then connected to a molex plug. as for hard drive space, i only had the rear cage filled so only 2 hard drives were installed on my mac.
last but not least was a quiet 70mm fan i put in place of the speaker hole. since i didn't use the internal speaker for anything, i removed it and put the fan in it's place. all that did was allow fresh air into the top for the psu fans.