Thanks donka for your tip. As of taking your advice, avoid using nVidia graphic card, my MacBook Pro late 2008 is back alive with lighting fast speed! 
This is what I did to avoid those “occasional freezes” and it does NOT even require clean install (sweet!)
- Go to System Preferences > Energy Saver > Select “Better battery life” from the selection of [Graphics:] at the top. This should be disabiling nVidia graphic card and using onboard GPU instead
- Also, DO NOT Connect SECONDARY MONITOR!! I was using mini-display port to connect Apple Cinema display as 2nd monitor. It works ok a while, but eventually, this occasional freezes come back.
With this settings, my MBP2008 boots within 4 gear spins and everything seems working great! It’s been nealy 40 hours since the new settings, 4 reboots, 3 hibernations, my MBP still works great.
BTW, I still keep the setting of “Put the hard disk(s) to sleep when possible” to trigger hibernate. Yes, it takes about 20-30 seconds to come back from deep sleep but occational sleep does not happen with this setting.
This may or may not work for other MacBook Pro late 2008 models, but it sure fixed my issue. I’ll look more into those secondary monitor issue if that really causes occational freezes.
Extra: Other settings I performed
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Disable chache for Safari
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Spotlight only against Mail
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Disable “noatime”
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Safeboot and Verify Disk (no error)
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PRAM Reset (it did not fix the problem before “Better Battery life” was set)
