Major disk manufacturers have usually provided their own diagnostic/repair tools. These run from Windows and/or a bootable CD and allow extensive surface testing, low-level formatting, and defective sector remapping. These tools don't generally care what kind of file system your disk contains, being concerned more about it's raw storage abilities.
When using a Windows operating system however, there are are a range of other issues that may arise - including accidental file deletion, junk file accumulation, and inefficient file storage (fragmentation). To deal with these, some of the most useful, well-designed, and professional-grade tools are by a company call “Piriform”. While all of their products can be reached from their home page, I've included more direct links with each description.
|SeaTools||Seagate's tool will work best with their own drives and those from Samsung, LaCie, and Maxtor (product lines acquired by Seagate)||Ignore the Windows version unless you have a dedicated workstation for testing multiple (secondary) drives.|
|Data Lifeguard||Western Digital's tool may work with Hitachi drives (acquired by WD) but the old Hitachi "Drive Fitness Test" is still available here.||Since only a Windows version is available, apparently you first need a working, bootable (Windows) drive in your PC to diagnose/repair a failing or non-bootable drive.|
|Recuva||If you have second thoughts about a file you just deleted - or even one you deleted last week - this might be able to get it back (or at least part of it).||It will also give you some idea why you should use something like DBAN before giving away your old PC. Note: If you have VSS taking periodic snapshots, ShadowExplorer may be an even quicker way to recover deleted files.|
|CCleaner||Cleans up temp files, caches, browser histories, and other files that waste disk space and potentially compromise your privacy.||Originally called “Crap Cleaner”. Also does registry and restore point cleanup. Of course, be careful you don't "clean up" things you are using - like your web password cache.|
|Defraggler||Defragments both files and/or free space to reduce excessive file access times caused by drive head "thrashing".||Oddly enough, even if your disk is half empty, files can still get fragmented. Note: Defragmentation is nearly worthless for a modern SSD used by Windows 7 or later - it could actually wear out the SSD faster.|