What I recommend is two things.
1. Test your system minus the boot drive (hdd) - unplug hdd from system. burn a memtest86+ iso (google it, easy to find) as bootable cd, and runt that overnight to test system and ram stability. it will catch 95~98% of system issues.
2. Test your hdd. go here:
http://www.tacktech.com/display.cfm?ttid=287 and find the brand of hdd to download and burn bootable iso image for your hdd. run a full erase (low level format, full format, etc) option and see if it finds any bad sector. Sometimes, full erase will fix some logical problems caused by incorrectly formatted drive issues. As long as the drive doesn't have any physical problem (bad heads, damaged platters, etc), it will work as normal again.
Even if the memtest passes, and hdd is normal, there is also a chance of mobo problem (such as sata controller, etc), in which case I recommend that you reset the bios on mobo, and try to switch sata connector on mobo (to another controller if there is more than 1). Basically try each sata port (0,1,2,3) to see if there is any difference. Also, use a new sata cable, as sometimes old sata cables causes data transfer issues.