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For the 40mm case fans we have the high quality and very reliable Noctua's 10mm and 20 mm thick versions, so if you have little space then take the thinner (10mm) one.
There are 2 versions the 3-pin and 4-pin. The 4-pin versions are with PWM. Our motherboards we sell have 4-pin headers, so please take the 4-pin version. With PWM the speed is automaticly adjusted. If you don't want to enable PWM take the 3-pin version. The fan will then most likely always run at top speed.
Our advice. Take the Supermicro Motherboard and connect PWM case fans to Peripheral zone fan headers and let PWM control the fan speed based on the PCH temperature.