I fully agree with what number_6 said. DIY noise abatement measures suitable for a home computer go against all a workstation stands for (warranty, reliability, etc.).

The Dell Precision 690 is actually reputed fairly quiet. No doubt the hard drives and graphics card fans are generating most of the noise. If I am not mistaken this model has a Mac Pro style layout, with passive CPU coolers vented by the case fans, which also have to remove the substantial heat contributed by the FB-DIMM's, so playing with the case fans may not be the best idea, lest airflow be excessively reduced.

The Quadro FX4500 is a ~110W card: no aftermarket passive (air-)cooler will handle that amount of heat. Another problem is that with two graphics cards, the fan on the first one is obstructed by the second card, probably forcing it to run faster. If the only reason for having two graphics cards is quad-monitor support, you'd be better off with passively cooled lower-end ones, or even one of those quad-head business-oriented Quadros or Matroxes.

As for the hard drives, soft-mounting them in empty 5.25" bays will help decouple their vibrations from the casing, although radiated noise will still be there; apart from the WD Velociraptors, all 10/15K rpm hard drives will be noisy, no way around it.