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Do you have your original OS X 10.6 install disc for troubleshooting purposes?
Restart your Mac
As soon as you hear the Startup chime, press and hold the SHIFT key
Continue to hold the Shift key until you see the Apple logo and progress indicator.
Then, let go of the Shift key and let it boot to the Desktop (it may take longer than usual so please be patient).
Can you run apps now?
If so, restart normally and test once more.