I was in a similar situation with an older SC846TQ chassis that I wanted to run with an X9SCM/E3-1230 and maybe 8~12 disks. The chassis was outfitted with 3pin fans (so no pwm control), and ridiculously loud power supply fans. I pretty much ended up gutting the chassis and rebuilding it with more up to date SM components (this is the great thing about the SM systems, they are incredibly modular).
I swapped out the power distributor (PDB-PT846-2824), replaced the 3 pin fan cables with 4 pin pwm cables (CBL-0216L ) as a starting point. I wanted to get the noise under control as much as I could and decided to go with active rather than passive cooling. As the chassis is 4U, that gave me quite a lot of freedom to pick a CPU cooler. I ended up using a Dynatron K17 which is a 3U unit with a 92mm fan, but there are a ton of options here. (I've also used the SM SNK-P0046A4 in 2U chassis for the X9SCx series of motherboards and they also work quite well in terms of noise and cooling ability)
In order to quiet down my chassis I first looked at the "whisper quiet 4U workstations" to see how they were configured ( they only have to support 8 drives so the airflow requirements should be somewhat similar). The quiet workstation chassis have the -SQ (super quiet?) suffix, and implement power supplies that also have the -SQ suffix. I went with the "PWS-920P-SQ" power supply. (N.B the redundant power supplies and power distributors in the various SM chassis are mostly interchangeable, but some of the larger rated power supplies have larger output connectors that require a different power distributor. The PWS-1K28P-SQ is one of the power supplies that has the "wide" connector, one reason to stick with the PWS-920P-SQ)
In terms of the mid plane fans, the
supermicro fan matrix is a great resource to see the specs of the fans. The 4U workstations use the "FAN-0074L4" which is a 0.58A 5000rpm fan (it is the only supermicro fan that I have come across that has a green housing). The typical 846 fans are the "FAN-0094L4" and they are 1.1A 6300rpm. The green FAN-0074L4 fans were a drop in for my chassis.
At the end of the day the active CPU cooler, lower rpm mid plane fans (FAN0074L4) and PWS-920p-SQ power supply quieted down my chassis no end, for what I consider to be a light to moderate load.
I've gone through all sorts of mods on my SM systems and have come to very much respect the designs and components that the SM engineers have chosen. Given the modularity of the chassis and components, my first line go-to items are always SM parts rather than "off the shelf" generic parts.