DiskWarrior has been the best tool to keep your Hard Drive away from trouble
Not only DiskWarrior keeps file directory catalog healthy, it also checks if you have bad sectors. Just running it once a month, your chance of loosing data drastically reduces.
The USB version of DiskWarrior contains OS X Utility. By booting off this USB, it is easier to Repair Permission, and you don't need to run maintenance from the Recovery Volume (Recovery Disk).
Note 1: Depending on the size of your hard drive, it may take something like 20 minutes. Unfortunately you need to be near since there will be a few prompt you need to attend
Note 2: When you see red text in the report, finish the process and run the same thing again. If you see the red text again, there is a chance your hard drive is damaged
Note 3: One of the prompt ask you to Save the Catalog File. This is not necessary since there won't be much usage for saved catalog file