Generally you can configure these as standard ports or for RAID 0 or 1. They will need a different controller and driver. These are capable of building a RAID array. These are becoming more popular but they do have a down side. I don't think these ports can be used for CD ROMs, DVDs and such but they do add expansion capability or RAID capability if you want it. If you configure a RAID array and want to load Windows on it, you will need to pre-install RAID drivers. If you use a RAID array as a secondary drive, you do not. Hope that helps.
Just bought a new mobo - Gigabyte GA-MA790FX-DS5
(spec here: http://www.giga-byte.co.uk/Products/Motherboard/Products_Overview.aspx?ProductID=2694 )
There are six SATA ports on the mobo:
4 x SATA II (orange ports - manual states: AMD SB600 controller)
2 x GSATA II (purple ports - 'Gygabyte SATA')
Manual quotes smae transfer rates and RAID setup but gives no indication as to why there are the two different SATA controllers!
Anyone know what if any diferences there are i.e. are there situations when use of one type benefits over the other??..........I guess there must be else why the two setups?!