I also have a tower with a lot of fans, and it was very loud. I cut a lot of the noise down by eliminating fan-to-case vibration.
1. If any of your fans are in big plastic enclosures that snap to the inner wall of the case, take them out and discard the big plastic enclosures. These enclosures do very little -- mostly they only restrict airflow and cause case-to-wall vibration.
2. Install small rubber O-rings between your fans and your case. That is, put the O-rings between the fan and the case wall. Thusly:
(http://pimpin-seattle.d2g.com/images/mj9/oring.jpg)
(Drawing not to scale)
This has the effect of separating your vibrating van from the case wall. When they're touching, the vibration noise is greatly amplified by contact with the case wall. When separated, there is no noticable loss of air flow, if the case wall is properly ventilated.
Also, rather than use metal bolts or screws to fasten your fans to the wall of your case, go get some plastic cable ties (http://www.rogerssystems.com/store/moreinfo.cfm?Product_ID=792&CFID=91704&CFTOKEN=60719320) (the ones that "zip" tight and can't be loosened) and use them instead -- they provide a snug hold on the fan and don't transfer as much vibration to the case wall as a metal bolt does.