With hard drives, don't worry about 3gb/s or 6 gb/s (SATA II v. SATA III) -- hard drives don't saturate even the 3gb/s connection, only SSDs do.
The higher rpm drive (10,000 rpm) does perform better as an OS and program drive compared to the 7200rpm, which in turn perform better than the green 5400rpm drives for that use. SSDs outperform HDDs as an OS drive, but cost more for much smaller sizes.
I use SSDs for data and programs, 7200 blacks for games and frequently used storage and green drives for backup storage that isn't accessed as often.