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Manufacturer software is the best.
Yes, many options. What it is your USB HD?
I like the hard drive testing applications that's included with Parted Magic. I prefer the version on Ultimate Boot CD.
Also keep in mind that many newer external drives come with a custom PCB that does not have a SATA connection. You may not be able to take it out of the casing and just plug it into a PC.
Here's how to run badblocks from a PartedMagic disk or USB stick:
http://hardforum.com/showpost.php?p=1039465768&postcount=14
Works on external USB drives just fine. Takes a LONG time.