Mountain Lion Mail & System Preferences are unresponsive

I have been having problems with my iMac Early 2009 for the last few weeks. We finally decided to replace the HD and reinstall OS. SO far we have not installed anything but OS 10.8.1 and the screen is getting these random dark squares, the System Preferences freezes and the Mail Program is constanlly crashing and unresponsive. I am now in the process of making a boot drive. But some how I have a feeling that it may be more than just a HD and memory Problem. I have checked VoiceOver as well as other things... Sigh... Can any one advise?

iMac (24-inch, Early 2009)

OS X 10.8.1 Mountain Lion

3.06 GHz

NVIDIA GeForce GT 130 512 MB