Run through this first
I have done a clean install twice, but it does not help.
Then if/when you clean install again (meaning no TimeMachine/clone restores) use the Disk Utility > Erase Zero or "middle" secure erase function on the entire drive (if possible) or just the Macintosh HD partition then install everything from fresh sources.
Sometimes the 10.6 boot disk (if your on that) can be a bit messed up, clean it with a bit of rubbing alcohol and a clean cloth to polish.
If only a bare bones install and fully updated still causes problems, then I would suspect a hardware issue that isn't being shown in Disk Utility > SMART or Hardware Test.
If the completely fresh install works fine, then cautiously add programs (fresh sources) and files to see if and when your troubles start again.