My assumption would be it does not matter.
I would use the 15 pin SATA power connector and leave the legacy 4 pin power connector available for other components in your computer system.
I have 2 raptors, 2 IBM Deskstars (to be retired when I get my data transferred), 2 CDRW, 3 fans, 1 eVGA 6800GT and one floppy so I need all the power connectors I can get my hands on!