I've been asking this exact question all over the net for a week now.
I want to do the exact same thing; install a SATA RAID card (3Ware 9650, 8-port) in the other other 16x slot.
I've gotten the same general answer, but not much "exact" help. Basically, from a PCI-E architecture standpoint, it should work.
But (there's always a "but") the particular MB in question (Abit/Gigabyte/MSI/whatever) might not like it and the only way to tell for SURE is to try it and see.
Not exactly what you want to do with $1K worth of RAID HBA and HDs.
Just to add to the archive/research value of this thread, I'll add this:
I'm currently debating b/t two MBs. One has two 16x slots (second slot is 4x electrical). The other MB has THREE 16x slots; two are 16x electrical, the third is 4X. <--Abit IX38 Seems to me (assumed by me...) that the third 4x slot is tailor made for another card BESIDES a graphics card. Sounds plausible, at least.
Problem is that the IX38 is brand new on the market. The other boards (IP35-based) have been out awhile and have mature BIOS/lots of updates.
I hate rolling dice.
*edit*
I just found this. Encouraging!
Abit IP35 Pro test report of devices tested in PCI-E slots.