Ran disk utility repair permissions....now I can not open any applications on my Mac mini

my Mac mini (mid 2011. OS X 10.9.1). Was running very slow so I ran repair permissions...after re-booting my computer I can not open any apple applications.  I keep getting a pop up window that says " finder quit unexpectedly". When trying to open safari " safari quit unexpectedly".  I can open skype, google chrome.   The computer indicates that wifi is on and connected - however I can't seem to log into Skype or access any web pages.  What to do next?
One more thing, I keep getting pop up windows asking for passwords for different items if or keychain...I have tried to put in my password, but that doesn't work. Not sure what password it is looking for but the window won't go away even when I hit cancel

Boot into your recovery partition (restart, hold down ⌘R until you see the Apple logo), and use Disk Utility to repair your hard drive.  OS X: About OS X Recovery
Then see if you can restart normally.

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