I agree with mikewhatever. Additional this might help:
The source shouldn't be damaged. The destination could be incomplete or so. If you want to see what was copied correctly and what not you can use
rsync -nrcv source destination
To get a list of files which haven't been copied correctly. Leave out the parameter
c to actually copy the data again.
To check a linux file system you can use
fsck (NTFS should be better checked by windows itself). To check all ext3 and ext4 partitions during next system boot you can use:
sudo touch /forcefsck
Don't use fsck on mounted partitions!
You can use the Disk Utility (run it form System / Administration or
ALT + F2 and
palimpsest). This is a graphical tool for hard disks and other storage devices. You'll find your harddisk there. Unmount it (there is a button there) and click Check Filesystem.