Put fan-speed controllers on your fans. Locate the temperature sensor in the outgoing air stream. This provides a constant temperature inside the enclosure (the fans only get noisy on really hot days), but requires some electrtical skills. I recommend "Wisp W-DC" from http://www.controlres.com (also distributed by ? Allied Electronics or Newark).
Buy a complete power supply, and specify a quiet ball-bearing fan, from Glitch-Master: this also provides over 0.25 seconds ride-through during power outages. See http://www.glitchmaster.com.
Switch to an ATX-style enclosure & power supply. The ATX power supply fan is located deeper into the power supply (on the interior surface of the supply, near the CPU), instead of being located on the back wall of the PC enclosure.