MHDD is the most popular freeware program for low-level HDD diagnostics.
MHDD supports these interfaces: IDE, Serial ATA, and SCSI. Also there is a possibility to access USB storage; there are drivers for emulation (USB->SCSI).
This software can make precise diagnostic of the mechanical part of a drive, view SMART attributes, and perform Low-level format, bad sector repair, different tests and tens of other functions.
More information on: http://hddguru.com/content/en/software/2005.10.02-MHDD/