WD brand is a good choice, as is Hitachi, but stay away from Seagate drives as I'v had failures on those (four of them) in less than six months.
I wouldn't advise going beyond 1TB though as the technology behind multi-terabyte drives is still too new to trust.
Better to have three separate 1TB drives like I have than a single 3TB one in my opinion. I keep the same data on all three drives to avoid data loss.
Sorry, know nothing about thunderbolt. never heard of it.