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Neither are "true" hardware RAID, but for RAID 0 or 1, there's very little processing overhead. It's parity calculations that are worthwhile to offload, such as those for RAID 5.
Unless either one has problems with the implementation, if all else is equal, the nVidia RAID will be faster, because it is integrated into the chipset and not limited to the bandwidth of the external PCI bus.
The SI RAID controller, though soldered to the motherboard, is really just hardwired into the same PCI bus that serves the PCI slots, and so is limited to 133 MB/s or so, in total. In practice, you'll be lucky to get 120 MB/s, and that'll be shared with all other PCI devices (audio, perhaps ethernet, etc.).
The nVidia RAID controller that's physically integrated into the chipset benefits from much faster connections, and should be able to support the full STR of both Raptors and the PCI bus simultaneously.
However, this is all theoretical. If there's a problem with the nVidia RAID implementation, then there's no huge penalty in using the SI controller to avoid that problem. But unless I knew of such a problem, I'd use the chipset SATA controller.
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