Interesting information here from MS:
The disk drive numbers may not correspond as expected to the SATA channel numbers when you set up Windows Vista, Windows Server 2008, Windows Server 2008 R2, or Windows 7 on a computer that has multiple SATA or RAID disks
That's for Server 2008 / Win7 - there's a somewhat similar article on server 2003 / XP here:
Overview of PNP enumeration and hard disk drive letter assignments in Windows Server 2003 and Windows XP
Basically, with more than one HD controller - SATA or PATA - you will get "interesting" PnP disk enumeration effects.
As I recall, MS used to define the "system" disk as the one with boot.ini (and other things like NTLDR) on it, and the "boot" disk as the one where the Windows system files reside. That's how I recall it from NT 3.5, anyway. Maybe they've changed it around, or maybe my memory is faulty! I've long since thrown away my NT3.5 resources, so I can't check it.
SD