I have favored the black drives since they appeared for SATA-II. They always cost a little more. I think the difference between the blue and black drives is the traditional cache memory in the drive.
Somehow, the blues seemed a bit noisier. I think I had one fail -- can't be sure. I generally order more than one drive of a kind when I need one.
With my ISRT SSD-caching configuration, I'd probably be OK with using the Blue WD HDD. An accelerated boot drive under ISRT doesn't have to work as hard as an HDD standalone.
Otherwise, I'd pick the Black drive for a standalone boot HDD. Also, successive generations of the same "badge" or model get different performance and reliability reviews.
There was also a 1TB Samsung drive -- I purchased three for my WHS-2011 server box. Think it was "Spinpoint," but I can't find them on the Egg. They may even have been SATA-II.
Call me an old fart, but I don't see the need for a 2 or 3TB boot drive. If filled to 66% or something of that order, you'd need a comparably sized drive to clone or back up. For data -- like recorded movies with Media Center -- maybe -- yes. But programs? Business data? Even photo collections? Rather doubt it.
My boot drive is 600GB, and only 252GB of space is filled after almost three years. Of course, I store documents, photos, movies, other data files on my server. The other HDD for the same system is 500GB -- used for DVR movie recording. Only 300GB are filled, and I have a LOT of movies and recorded TV shows. I prune these recordings from time to time.
Figure I've got computer files that go back to 1990. It's nice to have 2TB of storage, but I don't see myself running out of space anytime soon.