Not sure if it is the right tool (not sure what exactly you need inn technical aspect), but perhaps you may check out holodeck which main functionality is fault injection into any library. See http://sisecure.com/holodeck/
?:the art of a constructive conflict perceived as a destructive diagnose.
As someone who used to do this type of testing (for that little old Disk Utility Software company in Santa Monica) for DOS based apps. I would say you will need to build your own tool(s). That is what we did.
We had a program that would 'clone' a chunk of data or a file across a drive and do it in random order (thus fragmenting the drive). Another thing we would do is use the Disk Editor to directly edit the FAT on the system to cause/create cross-linked files (we would screw up the first instance of the FAT to see if DiskDoctor would catch it and use the 2nd instance of the FAT to fix things).
You will need to get information on the File Management system for the OS's you are testing on. That way you will know how to 'screw up' the disk. Have fun.