Depends on the clicking...
Some clicking may occur normally during reads and writes on some drives, however in my experience not on the WD Green drives. If it is pretty loud sounding it could indicate misalignment or the starting of motor failure which would definitely indicate a coming disaster.
I know the dilemma (about backing up) however, I would have to disagree with you on the time. At least when copying to another drive you can treat it like a Ronco oven - set it and forget it. When re-ripping your BD's you will have to physically insert/swap and set selections in the ripping software, etc... often that time alone will make it worthwhile as opposed to copying to/from an external device which, although painfully slow, can at least be doing its thing while you are asleep or working, etc..
If it's still under warranty and you're sure that you'd just as soon re-rip if it failed as opposed to backing it up now (but I would recommend checking to make sure that you don't have anything you can't re-rip like downloaded content backed up) - then I'd say just run with it until it dies or get's close to the end of the warranty period. If it doesn't fail during that period, just get a warranty replacement when it's most convenient for you - like during a time when you're going on vacation or going to be working a lot. That way you won't miss having access to them during the 2-6 weeks it can take for the warranty replacement process.
One other possibility which is more expensive, but will solve everthing and give you a bonus at the end: buy a SATA-USB enclosure from newegg or local store (cheaper the better pretty much) and a new HD. Replace the current drive with the brand new one, and put it in the external enclosure - set it to copy everything over while you're sleeping (a 2TB drive full shouldn't take more than 10-12 hours to copy everything even over USB 2.0).
Now do the warranty replacement on the drive and send it back... you still have everything, and no matter how long it takes - when it arrives back at your house you will now have external backup and/or additional capacity if you put it back in your HTPC as an internal. As a side note... on some warranty RMA forms, they require that you run a utility on the drive to see if it really has an error. Although not entirely honest, I usually just select whatever option they have for "I cannot access the drive at all" which will then skip all of this and get you a number. Since they never actually check the drives - it's way cheaper for them to just recycle/remanufacture the drive and send you a new one than to check every RMA.
