Heat and Noise

Assuming I go for a four hard disk setup there is a lot of heat to be dissipated from the hard disks and the CPU.

The following can be done to maximize cooling and minimizing noise
1. Use large hiperformance fans - atleast 120mm.
2. Low powered CPU's or underclock a power efficient CPU.
3. Enable power management on the hard disks
4. Don't mount all hard disks if you are not using them in real time.
5. Use onboard graphics card if you need it or get a motherboard without one and plug in a graphics card temporarily.
6. Make sure your setup has thermal sensors for all critical sections
7. Add a intake fan - it is better to have more fans running at slow speed than less fans at max speed.
8. Energy efficient PSU - atleast 85% or more if possible.
9. Green hard disks - they will have lower throughput but then they also conserve power in the long run.