I do not completely agree with your statements.
For a system disk I would choose a WD Raptor 10.000 RPM disk, either the 74 or the 150 GB.
For storage I would go for an Areca SATA2 controller, either the 1120 PCI-X or the 1220 PCI-e and use 8 Hitachi SATA300 disks in a Raid 5 or even preferably a Raid 6. With 500 GB disks, you would still end up with 3 TB of effective storage, even when 1 or 2 disks die on you and you can rebuild easily. Areca is significantly faster than 3Ware or other Raid controllers. Supermicro has a nice case with 8 hot swappable bays that would meet these suggestions.
Harm Millaard