I use a Rosewill docking station connected to my eSata port:
http://www.newegg.com/Product/Product.aspx?Item=N82E16817182197With Samsung 2TB drives:
http://www.newegg.com/Product/Product.aspx?Item=N82E16822152245Rosewill isn't a brand known for it's quality; but with it being pretty cheap, I decided to give it a try or end up building an expensive raid array for my ever increasing need for more storage. I already had 4 internal drives being near full as well as another old comp full of drives on my home network. Had my fill of slow USB externals and chose to get an eSata docking station that I can hot swap drives when wanted. Been using it for over 6 months with no problems.
Since this dock isn't enclosed, there's no fan. But it couldn't be easier to swap drives.
I recommend SAMSUNG Spinpoint F4 HD204UI 2TB 5400 RPM drives. Seems the most reliable of the 2TB drives and the low RPM means it stays cool without need for fans. But surprisingly it has great transfer speeds:
Here's a speed test on my latest drive (also wanted to make sure it was aligned). Tested while running on my eSata Dock:


The access time is lacking due to the low RPM, but the transfer rate is better than my internal WD Caviar Blacks. Perfect for storage. With copying speeds near 100 MB/s and with it also being hotswappable, I rarely touch my USB external drives.
To be able to hot swap the drives, you need to use AHCI. But for some reason can't dismount eSata devices with my Win 7's 'Safely remove devices' utility. This is common, but there's a program called Hotswap that does allow it and also helps mount the new drive after switching.
edit:
Well, after reading the whole thread, I agree that USB 3.0 is a good way to go. I assume the reason why my dock is discontinued is because it also can use USB 2.0 and everything is switching to USB 3.0.
But if you want to hot swap (switch drives without rebooting), eSata is the way to go.
As for arrangement: If you just want your files in proper order when viewing to play, then
Otaku Media Manager is the way to go.
http://www.otakumm.com/Just took these screenshots to show off this awesome media player:
Tested it on the new hard drive as I was adding anime to it.Found this a few days ago from a post by Lisa Hayes on Hongfong. It's the open sourced MediaPortal using a My Anime plugin that gets info from AniDB. Updates your database, sorts in groups, and gives correct title for each episode no matter how it's named (not modifying original files or locations). I have no problems playing any of the anime, including the softsubs which are exactly the same.